The optical transmission does not change in the visible region with an average transmittance value of 72–81%. Conversely, in the near infrared (NIR) region, the plasmon frequency shifts towards the IR region upon increasing Al concentration in the grown films. Nominally undoped SnOAluminum-doped tin oxide (SnO Research in tin oxide   and Al-dO3 (ITO) . AlthougA wide variety of growth methods can typically be used for the deposition of undoped and differently doped tin oxide thin films, including magnetron sputtering ,21,22,23To assist the design of SnOding PLD , spray pding PLD ,34, sol-ding PLD , powder ding PLD , and ALDding PLD . HoweverPolycrystalline nominally undoped and Al-doped SnOn system ,30,37 onA detailed characterization study was conducted using a wide range of standard analysis techniques. The surface morphology of different samples was analyzed by field emission gun-scanning electron microscopy . Top-view images were processed using digital ImageJ software in order to determine both the average and the biggest grain sizes in each film. The aluminum content in the prepared samples was estimated using an energy dispersive spectroscopy (EDS) analyzer equipped with a FEG-SEM system and Electron Probe Micro-Analyzer . EDS analyses were performed at low acceleration voltage (6 keV) to limit the signal obtained from the substrate so that a low atomic number element in a low concentration could be detected. EMPA measurements were performed at three different electron beam acceleration voltage values  and the data were analyzed using the Stratagem program dedicated to the analysis of thin films . TransmiIn order to evaluate the incorporation of aluminum in the SnOThe Al/(Al+Sn) atomic ratio obtained from EPMA is presented in For the sake of simplicity for presenting the results and further interpretation and discussion, sample identification is given here by using Al/(Al+Sn) results from EPMA, summarized in The top view SEM images of nominally undoped SnOThe SEM image of nominally undoped SnO4·5(H2O) ,29,39, a(H2O) [2 . AlthougDue to the presence of both grains and twin boundaries in nominally undoped SnOTEM samples were prepared by scratching the surface using a diamond tip to scratch off particles on holey carbon copper grids. TEM analyses were performed to assess whether Al was completely incorporated into the tin oxide lattice structure or rather was incorporated as a secondary crystalline Al≥1000 °C .SnOSince as deposited SnOSimilar to the as-deposited SnO present ,42, whicThe The XRD patterns of probed samples exhibit a systematic shift to higher degree and a broadening of the peaks upon increasing Al content in tin oxide films. To show this phenomenon, the (101) and (211) diffraction peaks were selected and plotted for all samples, in This shifting of the XRD peaks of tin oxide films upon increasing Al(acac)a and c) of tin oxide films versus Al atomic (%) in the film is presented in a and c were determined from the Equation . As the dopant concentration increases, both lattice constants decrease considerably and the relative decrease in c is almost double that for a. To confirm whether the evolution of the lattice parameters upon doping follows Vegard’s law [a and c follow Vegard’s law rather well.The errors both in determining the lattice parameters from different diffraction lines and the Al atomic (%) from EPMA measurements are included in the plot. Without doping, the lattice constants of SnOrd’s law ,45, whicIt has been stated that the electrical and optical properties of SnOtexture) . Thus, atexture) ,46,47,48N represents the number of reflections, in our case N = 7.As dopant ions substitute the host ions, the film growth orientation is altered as a result of mechanical strain induced in the lattice ,50,51. Hs method . The texBasically, for randomly oriented samples, the texture coefficient and degree of preferred orientation equal 1 and 0, respectively. In contrast, for perfectly oriented grain samples along the (hkl) direction, the texture coefficient equals N for (hkl) planes (N = 7 in our case) and 0 for other crystallographic planes and consequently the degree of preferred orientation is The pronounced structural reordering correlated with the evolution of texture coefficients for each (hkl) crystallographic direction and the degree of preferred orientation of the studied films are shown in wn films .It is further shown that the relative intensity between different (hkl) Bragg reflections is strongly dependent on the amount of Al incorporated into the growing film. The degree of preferred orientation is drastically reduced from 1.53 in undoped SnOFilms deposited on silicon wafer substrates were further examined by FTIR and the results are presented in ibration ,54, whiloworkers  reportedThe total transmittance spectra of nominally undoped and Al-doped SnOn is charge carrier density, e is elementary charge, In the spectral range of relevant electromagnetic wavelengths for the applications in which TCOs are used , free electrons dominate the electrical and optical properties. These properties can be described in a first approximation by the Drude free electron theory . This thFor highly doped TCOs, the plasmon energies are up to 1 eV, which is in the near infrared region of the electromagnetic spectrum. Due to the high number of free electrons, the incident infrared radiation is not transmitted but is rather reflected; this is a key feature for application of differently doped tin oxide thin films as low-emissivity window coatings.Conductivity of nominally undoped and the different Al-doped SnOOur nominally undoped tin oxide films prepared on different substrates have a conductivity of ≈1.1 × 10nditions ,22. Simi101 S/cm , and tha [0 S/cm . The hig lattice ,59. In attice [2 ,61, whicnn) of the same films. Their results showed that for unintentionally doped SnOnn) have the same values. Thus, they concluded that, within these experimental conditions, the carrier density can be even identified with chlorine content. Meanwhile, at a deposition temperature higher than 550 nIn order to address the actual role of the incorporated chlorine atoms with respect to the electrical properties, Messad et al.  performepy (AES)  and Secopy (AES)  observatpy (AES)  successfFor Al doped films, the scenario is different. Since AlHall effect measurements were possible only for the films with composition up to SnOThe relation between the charge carrier concentration and mobility is rather complicated in polycrystalline semiconducting materials . In genemobility . As we hSome reports claim ,35 that,In summary, we have presented a comprehensive study describing the change in structural, optical, and electrical properties of tin oxide thin films prepared by ultrasonic spray pyrolysis upon Al incorporation. The doping was possible by AlSEM images showed a decreasing grain size with increasing Al content in the prepared tin oxide thin films. In addition, Al doping drastically decreased the number of planar twin defects present in tin oxide films. EPMA analyses revealed that only ∼1/3 of Al present in the precursor solution is actually transferred into the grown films.Al doping also resulted in structural reordering of tin oxide by texture transition from (301) to (101), and then to (002) upon increasing Al content in the grown films. The optical transmittance of tin oxide was not changed in the visible region with an average transmittance of 72–81% being obtained. Meanwhile, a difference in plasmon absorption is observed in the near infrared region for all samples: the plasmon frequency shifted towards the IR region as a function of Al doping concentration.Nominally undoped tin oxide films exhibit a conductivity of ≈1.1 × 10These findings help to improve the understanding of the effect of Al doping on the properties of tin oxide thin films, including structural, optical, and electrical properties. In addition, the gained knowledge can be transferred to modify the properties of highly demanded florine doped tin oxide (FTO) thin films.


Increasingly available multilayered omics data on large populations has opened exciting analytic opportunities and posed unique challenges to robust estimation of causal effects in the setting of complex disease phenotypes. The GAW20 Causal Modeling Working Group has applied complementary approaches  to discover novel causal effects of genomic and epigenomic variation on lipid phenotypes, as well as to validate prior findings from observational studies.CPT1A and triglycerides, as well as of RNMT and C6orf42, on high-density lipoprotein cholesterol response to fenofibrate. The CPT1A finding also emerged in a Bayesian network study. The Mendelian randomization studies have implemented both existing and novel steps to account for pleiotropic effects, which were independently detected in the GAW20 data via a structural equation modeling approach. Two studies estimated indirect effects of genomic variation (via DNA methylation and/or correlated phenotypes) on lipid outcomes of interest. Finally, a novel weighted R2 measure was proposed to complement other causal inference efforts by controlling for the influence of outlying observations.Two Mendelian randomization studies have applied novel approaches to instrumental variable selection in methylation data, identifying bidirectional causal effects of The GAW20 contributions illustrate the diversity of possible approaches to causal inference in the multi-omic context, highlighting the promises and assumptions of each method and the benefits of integrating both across methods and across omics layers for the most robust and comprehensive insights into disease processes. The question of causality—and the distinction between association and causation—lies at the heart of scientific inquiry. In genomic research specifically, the principal focus is on estimating causal effects of DNA sequence variants on downstream phenotypes, ideally revealing the underlying biological mechanisms and identifying novel treatment targets along the way. At first glance, the task of causal inference in genomics seems trivial: individual genotype is inherited following Mendel’s laws of segregation and independent assortment, and stays stable after conception, obviating such concerns as reverse causation, confounding (except for population stratification ), or othcis-) CpG sites [The challenge of causal inference is even more daunting in methylome-wide association studies (MWAS), which interrogate associations between variation in DNA methylation and disease phenotypes. Although MWAS findings suffer from some of the same pitfalls as GWAS (eg the “winner’s curse”), they are additionally vulnerable to reverse causation and effects of confounding variables, as most of the epigenome is not heritable  and can pG sites , potentiThe GAW20 provided an opportunity to infer causal relations between the genotype, longitudinal measures of DNA methylation, and metabolic phenotypes, collected in a large family study of lipid-lowering treatment with fenofibrate . In thisThe characteristics of the GAW20 data set, built from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, are described in detail by Aslibekyan and colleagues . Briefly2 measure that moderates the influence of outliers. Although most teams operated within established methodologic paradigms  [Table  or SEM) , 12, 13, or SEM)  created 2 measure that would be robust to outliers. The remaining 5 studies also considered effects of epigenomic variation, which was the primary focus of the 2 MR studies [The contributions from the Causal Modeling Working Group reflected considerable conceptual diversity. Broadly speaking, the teams aimed to strengthen the inferences that arise from observational studies reporting associations between DNA sequence or methylation variation and lipid phenotypes. In the case of Auerbach and associates, who only interrogated the genetic contribution to the phenotype, the team aimed to develop a novel R studies , 12 that studies  and Just studies  focused  studies  sought tHistorically, causality has been defined under 1 of 2 main frameworks, commonly referred to by their most distinctive features: potential outcomes  and direIn contrast, the directed graphs framework relies on deterministic laws of science for describing causal relationships. It follows that complete knowledge of the underlying mechanism of a phenomenon reveals any cause and effect relationships. In practice, it is often impossible to account for every possible relationship that might exist between a set of variables. Directed graphs take advantage of probability distributions and sequential events in time or space to simplify characterization of the data generating process. Li and associates  used mecEven though the interpretations of causality varied within the Causal Modeling Working Group, the teams came to the consensus definition of causal inference as the process that evaluates  competing explanations for observed associations between exposures  and outcomes . All analyses took place in the multi-omic setting of GAW20 data, which held several causal possibilities as summarized in Fig. N = 1105), particularly by the standards of MR analysis, hampered detection of statistically significant effects. An important step that all teams performed, but that can be often overlooked, was ensuring that the data was suitable for analysis through formatting and cleaning, such as checking Hardy-Weinberg equilibrium and/or minor allele frequencies and handling missing data. All teams adjusted for covariates  in their analyses to address bias resulting from confounding or the potential mediating effects of such variables. A special case of covariate adjustment necessary in GOLDN/GAW20 data is accounting for family relatedness, which is essential for producing valid estimates of effect in genetic studies. That was accomplished by implementing existing methods accounting for family structure [2 measure that was resistant to such influences and could be used to strengthen inference from traditional statistics.The first set of challenges for the Causal Modeling Working Group was presented by the structure of the GAW20 data set. The moderate sample size N = 15, partictructure , extenditructure . Potentitructure , 10, 13.rs964184 on both triglycerides and high-density lipoprotein cholesterol, and thus indicating existence of true pleiotropy.The validity of causal effects estimated by all statistical methods hinges on satisfying the underlying assumptions, which are not always empirically testable. For example, MR estimators must meet the general assumptions for any instrumental variable, which include a robust association with the risk factor (testable), no common causes between the genotype and the phenotype of interest , and no pleiotropic effects . To address the third assumption, Sayols-Baixeras and colleagues  used theSimilar problems exist in Bayesian network analyses , requiriThe SEM analysis by Justice and colleagues  assumes The likelihood inference proposal for indirect estimation (LIPID) developed by Li and colleagues  focuses Furthermore, both Li and colleagues  and AuerFinally, as all teams used linear regression models, all methods used in the Causal Modeling Working Group are based on the standard assumptions of error independence, homoscedasticity, and multivariate normality, as well as a linear relationship between the genetic/epigenetic variants and phenotypes that is unlikely to completely capture the underlying biologic complexity.Related to the issue of methodologic assumptions, many of the analyses used by teams required some form of subjective choices, such as weighted covariance matrix, the size of methylation probe sets  or SNP wAll analyses performed by the Causal Modeling Working Group faced a number of computation challenges, included but not limited to bootstrapping , 10, impCPT1A, captured by both MR (in GAW20 and elsewhere [CPT1A methylation, Sayols-Baixeras and associates [The multilayered data environment provided by GAW20 was suitable for numerous avenues of causal inquiry, spurring vastly different approaches that unsurprisingly produced different results. One exception to that pattern was the effect of triglycerides on methylation loci in lsewhere . Notablysociates  also shoCPT1A methylation➔ triglyceride relationship was hindered by the lack of a strong genetic instrument for the methylation loci. However, future applications of novel variable selection methods such as constrained instrumental variables [RNMT and C6orf42 on high-density lipoprotein cholesterol response to fenofibrate reported by Jiang and associates [The convergence of the 2 distinct approaches on the same finding showed that the potential outcomes and the directed acyclic graph paradigms are not irreconcilable. Indeed, researchers have identified a variety of conditions necessary to bridge the 2 frameworks , 22, 23.ariables  may be asociates  were subsociates  only modFAT1 and DCTN6 as having a significant effect on triglyceride phenotypes. These 2 genes were not among those examined in the other analyses of the Causal Modeling Working Group, which precludes direct comparisons with other integrative methods, such as with the structural equations models implemented by Justice and colleagues [FAT1 and DCTN6 are biologically plausible, and are annotated to lipid metabolism in the Database for Annotation, Visualization, and Integrated Discovery database [Dctn6 emerged as a target for “thrifty” metabolic programming [Although most analyses undertook a candidate gene approach, aiming to strengthen causal inference for already known loci, Li and associates  used thelleagues . Howeverdatabase . Furthergramming , demonstgramming , these fThe experience of the GAW20 Causal Modeling Working Group illustrated several challenges and promises of causal inference in the multi-omic data environment. Employing diverse strategies to identify novel causal genes or validate prior observational findings, GAW20 contributions showed that there is no statistical “silver bullet,” as each method is predicated on its own—often not directly verifiable—assumptions. Because true causal findings are likely to be detected by more than one algorithm, future causal inference approaches can benefit from integrating multiple methods with complementary strengths and limitations. Moreover, as the availability of omics data on large population increases exponentially, it is imperative that future efforts continue exploring novel ways of leveraging all available omics layers for robust causal inference, as well as increasingly more accurate modeling of complex trait etiology.


Purpose. To report a case of a young patient with a clinical condition suggestive of Leber’s hereditary optic neuropathy (LHON) confirmed by genetic testing.Material and methods. We present a case of a 21-year-old Caucasian male with bilateral visual loss. The patient complained of visual loss, initially in the right eye and two weeks thereafter in the left eye. Ophthalmological examination revealed visual acuity of 20/ 400 in both eyes, anterior segment of normal appearance, normal direct and consensual pupillary light reflexes, and absence of a relative afferent pupillary defect. Fundus examination demonstrated bilateral protruding, hyperemic, with blurred margins in the nasal quadrant papilla and reduced excavation, tortuous vessels, peripapillary telangiectasias. The optical coherence tomography (OCT) revealed bilateral increase of the retinal nerve fiber layer (RNFL) thickness and ganglion cell layer – inner plexiform layer complex (GCL-IPL complex) severely thinned.Results. The clinical suspicion of Leber’s hereditary optic neuropathy was confirmed by the 3460 mutation, which was identified on blood mitochondrial analysis. Meantime, the visual acuity decreased to CF in both eyes. We initiated treatment with idebenone (300 mg T.I.D.). After three months of follow-up, visual acuity was CF in both eyes, bilateral pupillary light reflexes within normal limits and optic disc pallor was noticed in both eyes.Conclusion. No visual recovery was noticed after one year. We recommended that the idebenone treatment was continued and the patient was followed-up further.  Regarding risk factors, no specific environmental precipitant for vision loss in LHON mutation carriers has been clearly identified [2]. Nutritional deficiencies (e.g. vitamin B12 deficiency [3]) might also play a role in disease expression through an insufficiency of important metabolic cofactors [2]. Patients are strongly advised to moderate their alcohol intake and not to smoke to minimize mitochondrial stress [3]. Various other systemic illnesses, medications, and toxins have been proposed as triggers for vision loss in the setting of LHON mutations [2]. The gender could also result from a combination of subtle anatomic, hormonal, and/ or physiologic variations between males and females [1].LHON is caused by a variety of maternal transmission mutations with variable penetration and it is characterized by bilateral, painless, acute visual failure in one eye that develops during young adult life. Males are four to five times more likely than females to be affected, but neither gender nor mutational status significantly influences the timing and severity of the initial visual loss. Similar symptoms appear in the other eye on an average of two to three months later. Fundus examination features disk hyperemia, edema of the peripapillary retinal nerve fiber layer, retinal telangiectasia, and increased vascular tortuosity. The most important characteristic feature is an enlarging central or centrocecal scotoma and as the field defect increases in size and density, visual acuity deteriorates to the level of counting fingers or worse. After the acute phase, the optic discs become atrophic  and non-arteritic [6] anterior ischemic optic neuropathies due to absent blood dyscrasias in our patient and the age segment of which he is part. We have also excluded multiple sclerosis and optic nerve and orbit tumors that rarely cause bilateral damage. Last, but not least, we considered LHON, which was confirmed by genetic testing three weeks later.Based on the anamnesis, the ophthalmological examination, and the OCT examination, the first stage diagnosis was optic neuritis in both eyes. In order of importance, different causes of bilateral papillary edema in a young adult . A number of pathologic factors have been implicated, including a reduction for ATP being produced by the mitochondrial respiratory chain, impaired glutamate transport, and increased levels of reactive oxygen species production, all of which ultimately trigger retinal ganglion cell death via an apoptotic mechanism [1]. Neurologic abnormalities such as postural tremor, peripheral neuropathy, nonspecific myopathy, and movement disorders have been reported to be more common in individuals with LHON than in the general population. A multidisciplinary approach for those affected individuals with extraocular neurologic features should be considered [1].The ocular pathology in LHON is limited to the retinal ganglion cell layer with the sparing of the retinal pigment epithelium and photoreceptor layers [2]. Histochemical studies of RGC axons have shown mitochondrial clustering in areas with a high density of repolarization sodium-potassium membrane pumps, and an abrupt decrease in mitochondrial numbers was seen posterior to the lamina cribrosa where myelination begins and energy-efficient saltatory conduction occurs [2]. This uneven distribution of mitochondria suggests an increased energy requirement and special vulnerability of the unmyelinated retinal and prelaminar portions of the RGC axons to bioenergetic failure in LHON [2].The selective vulnerability of the optic nerve and the retinal ganglion cells (RGCs) that comprise it, to mitochondrial dysfunction in LHON, may relate to uneven energy demands along each RGC axon [7]. Regarding the GCL-IPL complex, macular OCT revealed selective loss of the GCL-IPL complex thickness in parallel with the loss of the temporal peripapillary RNFL thickness [8]. The natural history of GCL-IPL thinning follows a specific pattern of reduction, reflecting the anatomical course of papillomacular fibers [7]. GCL-IPL thinning was detectable in the deviation map during the presymptomatic stage in the inner ring of the nasal sector and then it progressively extended following a centrifugal and spiral pattern  [7].Major advancements in understanding LHON were possible after the introduction of the OCT [Fig. 16) [7]. In terms of the RNFL, thickness changes in the early stage of LHON, this showing a specific pattern of early thickening and late thinning , RNFL thickness provides the most reliable information about disease progression. The temporal and inferior quadrants show the earliest involvement of swelling, whereas the superior and nasal quadrants are affected later on [7]. The pattern of fiber loss in LHON does not seem to be influenced by the specific mtDNA mutation [9].The RNFL swelling is likely to depend on the compensatory increase of mitochondrial biogenesis and/ or axonal stasis along the fibers, and this does not allow detection of optic nerve atrophy in the early stages of the disease [3]. The presence of melanopsin-containing RGCs was first noted in 1923 when rodless, coneless mice still responded to a light stimulus through pupil constriction, suggesting that rods and cones are not the only light sensitive neurons in the retina [10]. They represent a very small subset (~1%) of the retinal ganglion cells [11]. Melanopsin retinal ganglion cells resist neurodegeneration due to mitochondrial dysfunction and maintain non-image-forming functions of the eye in these visually impaired patients [11]. They contribute to the regulation of pupil size and other behavioral responses to ambient lighting conditions [10].The absence of relative afferent pupillary defect is another feature of LHON. A relative pupillary defect is caused by an incomplete optic nerve lesion or severe retinal disease. It is highlighted by the swinging flashlight test . The table below illustrates the response rate at treatment with idebenone of the three most commented mutations and their rate of occurrence in males and females. Other positive prognostic factors have been identified including an earlier age of onset (< 10 years), a subacute presentation with slow visual deterioration, and a relatively large optic disc [1]. Even so, most persons remain severely visually impaired and are within the legal requirements for blind registration [1].LHON is diagnosed by molecular genetic testing , a short-chain benzoquinone, is an anti-oxidant assumed to transfer electrons directly to complex III of the electron transport chain, thereby bypassing complex I, which is affected by all three primary mtDNA mutations causing LHON, and restoring cellular ATP generation [12]. According to this biochemical mode of action, idebenone may reactivate viable, but inactive RGCs in LHON patients [12]. Clinical safety and efficacy of idebenone in LHON have been assessed in one double blind, randomized, placebo-controlled study (RHODOS) [12]. A greater proportion of those in the treated group recovered vision compared with the untreated group, and the most consistent factor associated with visual recovery was an early initiation of treatment during the acute phase of the disease process [1].Idebenone (We noticed case particularities as it follows:9].• The rapid evolution of the visual loss, within one month – mean: 6 months [2].• The sudden onset of the visual loss of the second eye, only two weeks apart from the first eye – mean: 6 to 8 weeks [• The lowest prevalence of the 3460 mitochondrial DNA mutation.• It is hard to assess the evolution under idebenone treatment, since the 3460 mutation has a low prevalence, and there is insufficient data about it.• Since the 3460 mitochondrial DNA mutation, the importance of genetic testing of relatives has the highest penetrability in females.Financial DisclosureNone of the authors has any financial or proprietary interest to disclose.


This study aims to determine if light scatter parameters measured with spatial frequency domain imaging (SFDI) can accurately predict stromal, epithelial, and adipose fractions in freshly resected, unstained human breast specimens. An explicit model was developed to predict stromal, epithelial, and adipose fractions as a function of light scattering parameters, which was validated against a quantitative analysis of digitized histology slides for  However, it still remains a challenge for surgeons to obtain clear surgical margins, with 20% to 40% of patients requiring follow-up re-excision procedures.,,,A common technique to overcome this time barrier is frozen section pathology (FSP), where cut tissue specimens are flash frozen and mounted during the surgery, to have slides diagnosed by a pathologist before closing the surgical cavity. While this technique has shown some diagnostic value despite known imaging artifacts from freezing,,,–Wide-field optical imaging can provide rapid sensing of an entire specimen surface, and while it lacks microscopic resolution, it can provide molecular or morphological sensitivity.Therefore, the ultimate purpose of this study is to elucidate the relationship between clinically relevant histological features from optical reflectance signatures, and furthermore develop and validate a method to predict these histological features from optical signals. For this study, a cohort of 22.1ex vivo breast specimen imaging study conducted in the Department of Pathology at Dartmouth Hitchcock Medical Center (DHMC) was approved by the Institutional Review Board for the protection of human subjects as detailed in a previous publication.,An In total, 37 specimens were imaged, which represents an expanded dataset obtained from a previous study,2.2,lsqnonlin , which minimized the difference between measured reflectance and light propagation model predicted reflectance. For the forward light propagation models, diffusion theory in the spatial frequency domainThe SFDI system and light-scattering parameters are thoroughly described in previous publications.,,The resulting optical properties of interest quantifying light scattering were the phase function parameter 2.3rgb2hsv function in MATLAB (v2016a), and the color saturation was used to compare each stain’s affinity. Pixels with greater hematoxylin saturation than eosin saturation were labeled hematoxylin, whereas pixels with greater eosin than hematoxylin saturation where labeled eosin. Pixels without significant hematoxylin or eosin saturation . The mean epithelium, stroma, and adipose fractions are plotted as functions of 2.5binofit. A two-sided two-sample t-test was used to test statistical significance of differences in distributions.For the leave-one-out cross-fold validation (LOO-CV), performance metrics were calculated for all specimen lesion pixels and also specimen averaged values. The sensitivity, specificity, and accuracy were calculated for each of the three output classes for specimens and pixels, and CIs were calculated using the Clopper-Pearson method according to a binomial distribution using the MATLAB (v2016a) function 33.1Based on the fitted models described in Sec. From these optical property predicted histological fractions, a simple threshold-based tissue classification scheme was implemented. Pixels with adipose volume fractions Case examples for a typical invasive ductal carcinoma (IDc), fibroglandular, and fat specimen are shown in 3.2The quantitative results of the LOO-CV analysis to test the accuracy predicting stroma, epithelium, and adipose volume fractions from optical property measurements are shown in A complete report of the distributions of both optical property predicted and H&E segmented epithelium, stroma, and adipose volume fractions stratified by invasive cancer, fibroglandular, and fat pathologies is shown in 3.3A summary of the quantitative performance analysis of the tissue classification algorithm is shown in Confusion matrices tabulating the fraction of true versus predicted classifications of all specimens (left) and pixels (right) are shown in 3.4Side-by-side comparisons of the model predicted metrics and digitized H&E data are shown for a heterogeneous specimen in 4–,–Label-free light scattering measurements have shown sensitivity to morphological changes between malignant and benign tissues through a multitude of studies across a myriad of optical sensing devices over the last 20 years.Previous studies utilizing spatially constrained spectroscopic reflectance measurements have revealed the sensitivity of light scattering to breast tissue morphologies. Laughney et al.,,–,The physical origins of light scattering arise from spatial fluctuations in the refractive index over size scales both smaller and larger than the wavelength of light, each of which uniquely contribute to the spectral and angular intensities of light scattering.Although strong correlations between optical property predicted and H&E segmented histology metrics were found and shown to be diagnostically relevant, there are a few notable limitations with this technique. First the spatial correlations between the optical images and the H&E slide are not exact, as the tissue shrinks during the fixation process. Although lesion-based averaging was used to overcome this common limitation, a further issue is depth coregistration, as the H&E section represents a superficial slice of the tissue only a few microns in thickness, while the optical measurements have a depth sensitivity of a few hundred microns. The inexactness of the depth coregistrations was likely the dominant source variability in the model. Second, the endpoints of stroma, epithelium, and adipose volume fractions are imperfect for both the description for origins of scattering signals and the metrics to classify benign from malignant lesions. This imperfection was highlighted in ,As mentioned previously, there are many ultrastructural features not quantified through histology, such as chromatin packing, mitochondria density, and collagen reformation, which could greatly affect both the light scattering properties and pathological diagnosis. One such example is that benign associated stroma in human breast tissue was shown to be more strongly scattering than tumor associated stroma.In conclusion, it was shown that label-free light scattering measurements of freshly resected human breast tissue acquired with SFDI were explicitly related to and predictive of clinically relevant histology metrics, as quantified from digitized, whole specimen H&E slides. Three optical properties related the scatter density, spectroscopic scattering intensity, and directional scattering intensity were found to have a logistic relationship to the stroma and adipose volume fraction and a Gaussian relationship to the epithelium volume fractions. From these relationships, a predictive model was created and validated with LOO-CV, which demonstrated that the optical property predicted epithelium to stroma ratio was diagnostically relevant in distinguishing malignant from benign glandular tissue. With future development, this technology may aid in the surgical triaging of large, freshly resected BCS specimens.


Background: Deficits in social cognition are well-recognized in both schizophrenia and autism spectrum disorders (ASD). However, it is less clear how social cognition deficits differ between both disorders and what distinct mechanisms may underlie such differences. We aimed at reviewing available evidence from studies directly comparing social cognitive performance between individuals with schizophrenia and ASD.Methods: We performed a systematic review of literature up to May 22, 2018 on Pubmed, Web of Science, and Scopus. Search terms included combinations of the keywords “social cognition,” “theory of mind,” “autism,” “Asperger,” “psychosis,” and “schizophrenia.” Two researchers independently selected and extracted data according to PRISMA guidelines. Random-effects meta-analyses were conducted for performance on social cognitive tasks evaluating: (1) emotion perception; (2) theory of mind (ToM); (3) emotional intelligence ; and (4) social skills.Results: We identified 19 eligible studies for meta-analysis including a total of 1,040 patients (558 with schizophrenia and 482 with ASD). Eight studies provided data on facial emotion perception that evidenced a better performance by participants with schizophrenia compared to those with ASD . No significant differences were found between groups in the Reading the Mind in the Eyes Test , other ToM tasks , emotional intelligence , and social skills . Participants' age was a significant moderator of effect size in emotion perception and RMET analyzes, with larger differences favoring patients with schizophrenia being observed in studies with younger participants.Conclusions: The instruments that are currently available to evaluate social cognition poorly differentiate between individuals with schizophrenia and ASD. Combining behavioral tasks with neurophysiologic assessments may better characterize the differences in social cognition between both disorders. Social cognition concerns the detection, processing and use of social information to regulate interpersonal functioning and effective social behavior , 2. SchiIn schizophrenia, social cognition impairments have mostly been described in the following domains: (1) emotion perception, defined as the ability to identify emotions, for example from a facial expression or tone of voice; (2) theory of mind (ToM), defined as the ability to infer other people's mental states ; (3) attributional style, defined as the way by which individuals explain the causes of positive and negative events ; and 4) judgment, including the ability to extract meaning from environmental information, and the processing bias known as “jumping to conclusions,” which refers to the tendency to formulate definitive judgements based on insufficient confirmatory evidence  judgment. In turnPatients with schizophrenia and ASD have consistently been shown to perform worse than neurotypical controls in social cognitive tasks –13. In aWith respect to the “jumping to conclusions” dimension of social cognition, although it has typically been studied as a specific deficit of schizophrenia, at least one study by Brosnan et al. found that ASD subjects show a more circumspect reasoning bias , which is the opposite pattern of the jumping to conclusions reasoning bias observed in schizophrenia . The stuAll in all, it remains unsettled whether or not schizophrenia and ASD differ in terms of social cognitive performance , with thWe set out to review studies that performed head-to-head comparisons of social cognition in subjects with ASD and with schizophrenia. Our main goal was to identify differences in social cognitive performance between patient groups that could help characterize the specific social cognition impairments of each disorder. Understanding how social cognition differs between schizophrenia and ASD, and what underlying mechanisms explain such differences, may help develop disorder-tailored interventions which may potentially improve outcomes, as targeted social cognitive interventions have been shown to be especially effective in improving emotion perception and ToM .The research questions for this review were: (1) do direct comparisons of patients with schizophrenia and ASD show any differences in social cognitive performance? (2) do these differences in social cognition ability between patients with schizophrenia and individuals with ASD contribute to our understanding of the specific deficits and mechanisms that underlie social cognitive impairments in both disorders?We conducted a systematic literature review to identify studies comparing social cognition between patients with schizophrenia and patients with ASD. Comparative meta-analyses were performed for those social cognition dimensions that were directly compared between patients with schizophrenia and patients with ASD in at least 3 individual studies.We reviewed studies including groups of patients with schizophrenia spectrum disorders  and groups of patients with ASD , regardless of age or gender. We included any study comparing social cognition across these two groups of patients.The identification and selection of studies was conducted according to PRISMA guidelines. The following inclusion criteria were considered for the selection of studies for the meta-analyses:- Original articles in English, French, German, Portuguese or Spanish, regardless of publication date or country of origin;- Studies including human populations;- Any clinical studies directly comparing social cognitive performance between groups of patients with schizophrenia spectrum disorders and groups of patients with ASD.The search was performed on Web of Science, Scopus and Pubmed and the search strings used were formed from combinations of the keywords “social cognition,” “theory of mind,” “autism,” “Asperger,” “psychosis,” “schizophrenia” and the Boolean operator AND. The search was concluded on May 22, 2018.After eliminating duplicates using Mendeley library tools, two researchers reviewed the list of articles separately, selecting eligible reports according to the criteria defined. Abstracts from scientific meetings and conference proceedings were not considered eligible for meta-analysis, due to the frequently incomplete reporting of quantitative data and the risk of double inclusion of individual subjects in cases where conference proceedings were followed by regular publication of full articles in scientific journals at a later time.Two researchers extracted the following data from each eligible study: author and publication year, number of participants in the schizophrenia and ASD groups, mean age of each group, gender distribution of each group, mean intelligence quotient (IQ) of each group, psychometric outcome measures, summary of psychophysiological comparisons (where available), and any relevant additional information.t-value, or F-value from Analysis of Variance tests). Data were extracted either directly from the text and tables or extrapolated from figures. In the latter situation values (mean and standard deviation) were extracted using Adobe Acrobat Reader measurement tools. To account for measurement error, each value from each figure was measured five times, and the mean value computed. In cases where data included in the original manuscript were insufficient, we contacted the corresponding author to request further information.Psychometric outcome measures were classified according to the following social cognition dimensions: 1) emotion perception; (2) ToM (inferencing); (3) emotional intelligence; and (4) social skills. The outcome measures (tasks) that were used to assess each social cognition dimension are listed on Table  emotion Separate meta-analyses were conducted for each psychometric outcome dimension. When studies used more than one measure to evaluate the same social cognition dimension, the measure that was most frequently used in all studies was selected. When studies used psychometric measures that were not used in any other study, the measure that most approximated the measure used in the majority of the remaining studies, based on the provided task description, was selected by consensus, after reviewing the available literature on the psychometric properties of the instrument in question with regards to convergent validity with the most frequently used task.2 to estimate the ratio of true heterogeneity to total observed variation, and Tau2 (T2) to estimate between-study variance , with an I2 value of 72%. No missing studies were identified in the trim and fill analysis. Funnel plot analysis did not reveal marked asymmetry . Participants' mean age was found to have a significant moderator effect , with larger effect sizes for between-group differences (favoring better performance in the schizophrenia groups) observed in studies with younger participants  and ASD (n = 10) groups did not differ in emotion perception performance in a social scenes task where faces expressing a single emotion were either present or digitally erased, differences were found when eye tracking data were analyzed: individuals with schizophrenia oriented gaze to face regions more rapidly when faces were present relative to stimuli from which faces had been removed, while the autism groups oriented gaze to the face region at the same speed regardless of whether the face was present or not (n = 44) and ASD (n = 21) groups in emotion recognition accuracy. The two clinical groups only differed from the neurotypical control group when faces were presented integrated into congruent and incongruent emotional contexts, but not when faces were presented in isolation. Interestingly, while patients with schizophrenia and neurotypical participants showed increased fixation time to the face region when faces were presented within an incongruent emotional context compared to when they were integrated into a congruent emotional context, this was not observed in the ASD group, who spent the same time fixating the face region regardless of emotional context congruency. Moreover, in individuals with schizophrenia, emotion recognition accuracy correlated with IQ, while this was not the case in individuals with ASD (n = 92) were impaired in both auditory and visual tasks, participants with high-functioning ASD (n = 19) were impaired only in the visual emotion recognition task  and I2 was 79.20%. Funnel plot analysis did not reveal marked asymmetry . Age was found to have a significant moderator effect , with larger effect sizes (favoring a better performance by patients with schizophrenia) in studies with younger participants , and an I2 value of 75.76%. The funnel plot was symmetrical . Age of participants did not have a moderator effect on mental state inference ability (p = 0.993). Several studies included in this meta-analysis provided additional relevant information regarding specific aspects of ToM performance. Martinez et al. (n = 36) had a better performance than individuals with ASD (n = 19) in attribution of mental states using the Movie for the Assessment of Social Cognition (MASC) test, that assesses subtle inference abilities. Both groups performed significantly worse than neurotypical controls in the over-mentalizing measure of the MASC, showing a high number of wrong answers on the task that reflects overly complex mental state reasoning , suggesting that high levels of paranoia symptoms are associated with heavier compromise of ToM ability (n = 22) perform worse than men with Asperger's syndrome (n = 26) in the Intentionality score , while no such difference was observed in females. In contrast, women with schizophrenia (n = 14) performed worse than women with Asperger's syndrome (n = 27) in the Appropriateness Score (capacity to adequately describe the actions in an animation), with no differences between men of both groups in this measure , with an I2 value of 57.88%. Funnel plot and Egger statistic were not interpretable due to the low number of studies (data not shown).Three studies assessed emotional intelligence , 27, 31 p = 0.056; Figure 2 value of 82.84% and a highly significant Q-test value of 11.66 (p = 0.003), suggesting poor comparability between the different social skills measures used in the original studies. Funnel plot and Egger statistic were not interpretable due to the low number of studies (data not shown). In the study by Morrison et al. (n = 54) showed significantly less repetitive movements and asked significantly more questions than participants with ASD [n = 54] who, in turn, scored better on clarity and flat affect (n = 20) compared to patients with first-episode psychosis, while the latter showed higher scores in the Awareness  and Communication  subscales of the Social Responsiveness Scale . Additional sources of potential selection bias include the following: (1) diagnostic variability, with some studies including more broadly-defined psychotic syndromes and ASD; (2) differences in mean age across diagnostic groups, participants with schizophrenia being significantly older in 8 of the 19 studies; (3) differences in IQ across the two clinical groups, with higher IQs in ASD participants in 4 studies.Another frequent limitation found in studies included in the meta-analyses concerns the absence of measures to reduce measurement bias. Most studies do not mention if raters were adequately trained in the application of social cognitive tasks or if they were blinded to the participants' diagnosis. Notable exceptions were: (1) Craig et al. who used a second blinded rater in the coding of a sample of transcripts of the Attributional Style Structured Interview (ASSI) ; (2) EacThe need for direct comparisons of social cognitive performance between patients with schizophrenia and ASD is amply recognized in the literature as a fundamental contribution to a better understanding of the similarities and differences between these two neurodevelopmental disorders . Here wep = 0.003). Furthermore, we found that age significantly influences the effect size of this difference in performance, so that with increasing age the difference in emotion perception ability between ASD subjects and patients with schizophrenia disappears. This may reflect, on the one hand, a deterioration of social cognitive skills in schizophrenia patients with increasing illness duration, and on the other hand an age-dependent improvement of emotion perception skills in ASD, probably as a result of social learning and accumulating social experience. Indeed, Lever and Geurts found that ToM deficits observed throughout adulthood in ASD were no longer present in older (50+ years) adults  adults , in a re) adults . Given t) adults  and that) adults , 66, 67,) adults .n = 13) that was not present in a comparison group of subjects with ASD (n = 15)  . Lysaker(n = 15) ; finally(n = 15) .Our meta-analysis found no differences between patients with schizophrenia and ASD in terms of mental state inference as measured by a variety of tasks and instruments. Where differences were found, they tended to favor a better performance by patients with schizophrenia compared to those with ASD , 35, 36,Specifically regarding schizophrenia, there seems to be converging evidence that mental state inference skills are critically influenced by the severity of clinical symptoms of this disorder, namely disorganization , paranoiMeta-analyses of studies comparing social skills and emotional intelligence between ASD subjects and patients with schizophrenia also showed no difference between the two groups on these measures of social cognition, although, due to the low number of studies in each analysis, these were likely underpowered to find small or moderate effect sizes.Together, the reviewed literature suggests that, other than in the ability to recognize emotions from perceived faces  there seem to be no clear and consistent differences between ASD and schizophrenia in terms of social cognitive performance. There are at least three possible explanations for this: (1) ASD and schizophrenia are partly overlapping disorders with partly overlapping social cognition deficits and partly overlapping neurobiology; (2) social cognition deficits in ASD and schizophrenia are the final, common outcome of differing developmental pathways and neurobiological mechanisms; (3) the instruments that are in common use to assess social cognition in these two disorders lack the necessary specificity to discriminate between them, or at least are not sensitive enough to qualitative differences between the two disorders. It is likely that all three explanations are valid. Schizophrenia and ASD are two severely impairing neuropsychiatric disorders with partly overlapping genetic risk, and partly shared neurobiological abnormalities , 19. WhiFinally, many studies have found that despite being quantitatively similar, the social cognitive deficits found in ASD and schizophrenia are qualitatively distinct. For instance, social cognitive impairments in schizophrenia are heavily influenced by attributional bias in schizophrenia, while in ASD apparently similar social cognitive impairments predominantly correlate with a hypomentalization bias, where social stimuli and information are given lower relevance for making social judgements .The importance of exploring differences and similarities in social cognition between schizophrenia and ASD has more than just theoretical implications. A better understanding of the mechanisms that underlie and differentiate social cognitive impairments in the two disorders will help develop disorder-tailored interventions that are capable of improving social functioning. Currently available evidence from direct comparisons suggests that interventions aiming to improve social cognition in schizophrenia should consider the importance of concomitant cognitive impairments and clinical symptoms, which should be adequately addressed in order to maximize gains from the interventions aimed at social cognitive skills. Lindenmayer et al. have previously shown that the combination of cognitive remediation with social cognition training is associated with better intervention outcomes than cognitive remediation alone . Conversn < 30), a frequent feature of social cognition studies. Such limitations are further compounded by the inevitable uncertainty intrinsic to attempts at meta-analyzing studies in such a broad and subtly complex field as social cognition, marred by an apparent infinity of measurement tools and concepts whose similarities and boundaries are not always clear. Notwithstanding, we opted to conduct a meta-analysis of direct comparisons between participants with schizophrenia and ASD rather than a solely descriptive review, based on the following reasons: (1) several meta-analyses have been conducted in the past regarding social cognition in patients with schizophrenia  Studies that compared social cognitive performance in ASD and schizophrenia show that individuals with ASD perform significantly worse than individuals with schizophrenia in emotion recognition tasks, and that this difference becomes less pronounced with increasing age. With respect to other dimensions of social cognition, available evidence is contradictory, and aggregated data do not show meaningful differences between the two diagnostic groups. It is currently not clear whether this absence of significant differences reflects shared disease mechanisms or an inability of currently used instruments to detect subtle, qualitative differences. On the other hand, study heterogeneity and the complexities of assessing social cognition caveat against overstating the reliability of aggregated data analyses in this field. Future studies addressing this question should be based on larger and more homogeneous samples, and should ideally accompany the assessment of social cognitive tasks with other measures, namely neuroimaging and neurophysiologic measures such as eye-tracking or event-related potentials. Such studies will contribute to a better understanding of the mechanisms that are specific to each disorder, and will pave the way to the development of more specific and hopefully more effective therapeutic interventions aimed at improving social skills in each of these disorders.JB-C, RJ, and JF planned and designed the study. JF and RC conducted the literature search and selection of articles for the review. JF and RC extracted data from eligible studies. JF and JB-C conducted data analysis. JF, RC, RL, and JB-C were responsible for drafting the introduction, methods and results sections of the manuscript. All authors contributed equally for the discussion section and for the final review of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


TREM2) and Apolipoprotein E (APOE) are enriched in the innate immune system and modulate the neuroinflammatory response of microglia to tau pathology. Microglia can play an active role in synaptic dysfunction by abnormally phagocytosing synaptic compartments of neurons with tau pathology. Furthermore, microglia are involved in synaptic spreading of tau – a process which is thought to underlie the progressive nature of tau pathology propagation through the brain. Spreading of pathological tau is also the predominant target for tau-based immunotherapy. Active tau vaccines, therapeutic tau antibodies and other approaches targeting the immune system are actively explored as treatment options for AD and other tauopathies. This review describes the role of microglia in the pathobiology of tauopathies and the mechanism of action of potential therapeutics targeting the immune system in tauopathies.Tauopathies are a heterogenous class of diseases characterized by cellular accumulation of aggregated tau and include diseases such as Alzheimer’s disease (AD), progressive supranuclear palsy and chronic traumatic encephalopathy. Tau pathology is strongly linked to neurodegeneration and clinical symptoms in tauopathy patients. Furthermore, synapse loss is an early pathological event in tauopathies and is the strongest correlate of cognitive decline. Tau pathology is additionally associated with chronic neuroinflammatory processes, such as reactive microglia, astrocytes, and increased levels of pro-inflammatory molecules . Recent studies show that as the principal immune cells of the brain, microglia play a particularly important role in the initiation and progression of tau pathology and associated neurodegeneration. Furthermore, AD risk genes such as Triggering receptor expressed on myeloid cells 2 ( Pathological tau protein is observed a wide range of neurodegenerative disorders (NDD) and is the key defining feature of a heterogeneous class of diseases called tauopathies. Alzheimer’s disease (AD) is the most common tauopathy - affecting approximately 45 million people worldwide – and is additionally characterized by extracellular plaques composed of amyloid beta (Aβ) . Less coMultiple cell types can have immune functions in the brain, for example microglia, astrocytes, perivascular macrophages, meningeal macrophages, choroid plexus macrophages, and infiltrating peripheral myeloid cell types . However(MAPT) gene on chromosome 17q21.31, and this gene can be mutated, inverted, duplicated, and abnormally methylated. All these modifications have been associated with increased risk of developing tauopathy and the genetic evidence therefore clearly links tau to neurodegeneration [Tau is an abundant protein that is predominantly expressed in the axonal compartment of neurons, but also at lower levels in oligodendrocytes and astrocytes . The maineration , 176.MAPT gene [. The six isoforms in combination with the multitude of potential PTMs make the biology of tau extraordinarily complex. Belonging to the class of natively unfolded or intrinsically disordered proteins, tau proteins lack clearly defined secondary and tertiary structures.The human brain contains 6 isoforms generated by alternative splicing of exons 2, 3 and 10 of the APT gene . Tau canAPT gene . Tau proAPT gene , 325. ThThe MTBR of tau contains two hexapeptides that can form intermolecular beta sheet rich structures: aa275–280 (VCIINK) in R2 and aa306–311 (VQIVYK) in R3 , 308. PaSmaller tau oligomers are still soluble and can mislocalize to the somatodendritic compartment to cause toxicity throughout the cell . For thiNeuronal stress or neuronal damage induced by intracellular tau pathology can also impact nearby immune cells, such as microglia . FurtherMicroglia are the tissue resident macrophages in the brain and originate from yolk-sac-derived erythro-myeloid progenitors . Their uDuring neurodevelopment, microglial contact induces synapse formation in the cortex . FurtherMicroglia also play an important role in maintaining synaptic structure and function later in life. Microglia are for example required for maintenance of synaptic structure and synaptic transmission in the adult retina . MicroglTREM2 only leads to impaired response of microglia to injury in old mice [When trying to understand the effects of pathological protein aggregates such as tau pathology on the brain, it is important to note that in humans these effects are often superimposed on the normal effects of aging. In rats, for example, viral delivery of tau protein to young and aged animals led to more microgliosis, neuronal loss, and behavioral deficits in the aged group . It is told mice . Furtherold mice .Microglia not only respond to the aging cells around them but also display signs of senescence themselves in the aging human brain , 292. In. As will be described in more detail later, tau pathology is also robustly associated with activation of classical complement cascade and the release of pro-inflammatory cytokines such as IL1B, IL6 and TNFa [In AD, microglia were previously predominantly studied in the context of plaque pathology and plaque-associated microglia were indeed already observed by Alois Alzheimer . Howeverand TNFa . A varieThe most obvious one is that tau aggregates directly activate microglia. Tau oligomers co-localize with microglia, astrocytes, and pro-inflammatory cytokines in the brains of tauopathy patients and transgenic mice . When apInterestingly, application of AD-derived soluble tau to cultured microglia causes their degeneration , 257 andNeurons that are trying to cope with tau pathology express factors such as Cx3Cl1 acting on microglial receptor Cx3cr1 . This siThe effects of tau pathology on microglia may also be mediated by the vasculature. Tau pathology leads to vascular inflammation and alterations of blood vessels , 210, whRhoA specifically from microglia led to microglial activation, astrogliosis, increased transcription levels of pro-inflammatory cytokines, neurodegeneration, and accumulation of hyperphosphorylated tau in wild-type mice [Whether inflammation is a cause, a contributor, or a consequence of tau pathology is one of the central questions relating to the role of microglia in tauopathies . Severalype mice . This suype mice . These sAdministration of anti- or proinflammatory stimuli or compounds has been used to demonstrate that microglia and inflammation are linked to tau pathology. Treatment of mouse models of tauopathy with anti-inflammatory drugs led to a decrease in tau pathology , 322. FuInduction or exacerbation of inflammation is also likely linked to tau pathology. Both administration of LPS and virus-induced inflammation led to increased hyperphosphorylated and insoluble tau in 3xTg mice and this effect could be rescued by blocking the kinase GSK-3B , 294. LPOne consistently upregulated pathway in tauopathies is complement . The comThe complement pathway has been studied at multiple levels in the context of tau pathology. For example, overexpression of natural C3 inhibitor sCrry was found to decrease tau pathology . AccordiThe mechanism of inflammation-induced tau pathology seems to be at least partly mediated through the direct effect of pro-inflammatory cytokines. The best characterized cytokine involved in this regard is IL1B, which is cleaved into its active form by caspase 1 – downstream of NLRP3 inflammasome activation . Indeed,Microglia can phagocytose extracellular tau, and aggregated or hyperphosphorylated tau is observed in microglia of mice and humans with tau pathology , 238. FuAPOE (apolipoprotein E) ε4 and TREM2. APOEε4 is a common variant of the APOE gene and the strongest risk factor for LOAD. TREM2 risk mutations are substantially less common than the APOEε4 allele, but their risk effect for LOAD is almost of the same magnitude [TREM2-dependent transcriptional network in disease-associated microglia (DAM) that is associated with a wide range of disease and neurodegenerative conditions [IL1B, CCL2) and downregulate homeostatic genes . However, in contrast to the LPS-induced microglia, DAM upregulate other genes like APOE and TREM2. In addition to being part of the DAM genetic network, TREM2 and APOE have also been shown to physically interact with each other and this pathway was important for the phagocytosis of Aβ [TREM2 and APOE on tau pathology is at an early stage, but the findings so far will be discussed below.Many LOAD risk genes are predominantly expressed in the innate immune system and enriched in microglia . The resagnitude . Interesnditions , 172. Innditions , 309. This of Aβ . Interesis of Aβ . Howeveris of Aβ . The resTREM2 gene knock-out in the mild hTau model that expresses all six human isoforms led to exacerbation of tau pathology [TREM2 in the more aggressive PS19 mouse model at later stages showed a marked reduction in neurodegeneration and DAM-associated genes [TREM2 is a transmembrane receptor of the immunoglobulin-superfamily that in the brain is predominantly expressed on microglia. Activation of TREM2 leads to interaction with its adaptor protein DAP12 . The ITAM domain of DAP12 recruits SYK, which activates signaling cascades that are involved in metabolism, survival proliferation, and phagocytosis . TREM2, athology . Howevered genes . Surprised genes . Knockoued genes , which wAPOE is a lipid carrier that is predominantly expressed in astrocytes and to a lesser degree in microglia. The human brain contains three different alleles: ε2, ε3 and ε4. One copy of ε4 increases AD risk by about 3 times, whereas ε4/ε4 increases risk 12 times . SurprisIntracellular tau pathology can damage the synapses from within via a multitude of pathways . AggravaIt is unclear how tau pathology leads to C1q-mediated tagging of synapses but a possible pathway could include local apoptotic mechanisms, leading to the exposure of phosphatidylserines on the synapse to which C1q can bind , 123. FuTau pathology-induced alterations in microglial secreted factors may also adversely affect synaptic function. Microglia in the adult brain are important for learning-induced synapse formation via secretion of neurotrophic factor BDNF . MicroglMicroglia also have bidirectional signaling cascades with astrocytes. Astrocytes are a highly heterogenous population that make up approximately 20% of brains cells and are derived from the same progenitors as neurons . AstrocyTau pathology can lead to synapse loss via a decrease in neurotrophic thrombospondin signaling by astrocytes . In addiGiven the increasing recognition of microglia as central players in the pathogenesis of tauopathies, it is perhaps not surprising that there is increasing interest in targeting inflammatory pathways for these diseases Table . Anti-inImmunotherapy directly targeting tau protein has also emerged as a promising approach in the treatment of tauopathies and microglia have been increasingly recognized as an important player in the mechanism of action of immunotherapeutic approaches . Active Most research has focused on the development of antibodies that neutralize extracellular tau and inhibit synaptic spreading of pathological tau , 320. TaMicroglia are fascinating cells and the large number of excellent recent studies demonstrates increasing recognition of microglia as critical players in the pathobiology of tau protein. It is currently not fully resolved if inflammation is a cause, contributor or consequence of tau pathology. Pro-inflammatory mediators secreted from microglia  can initiate tau pathology and play a critical role in tau-induced neurodegeneration. The strongest evidence for inflammation-induced initiation of tau pathology currently exists for TNFa, as this cytokine was shown to lead to formation of tau aggregates in neurites . More prMicroglia are also directly involved in tauopathies as they have been shown to pathologically phagocytose synapses of neurons with tau pathology. Currently, the pathways underlying microglia-mediated synapse loss are not fully characterized and a multitude of potential pathways have been identified in neurodevelopment. Complement-mediated synapse loss via microglial synapse phagocytosis under neurodegenerative conditions is now described in multiple disease models. However, it is not known what causes the binding of C1q to synapses and if this happens indiscriminately or only targets vulnerable synapses. In neurodevelopment, there are signals (e.g. CD47) that protect synapses from microglial pruning. We need to understand better the function of these signals in the normal brain and determine if they are downregulated in response to neurofibrillary pathology. Additionally, since astrocytes play a critical role in both synaptic function and neuroinflammation, more studies are needed on bidirectional microglia-astrocyte signaling in tauopathies.As principal macrophages of the brain, microglia phagocytose tau and may play a role in spreading tau pathology throughout the brain. Determining the exact contribution of microglia to the disease pathogenesis remains an important topic for future investigations. More studies are needed on the mechanisms of tau internalization in microglia and if this is associated with activation of pro-inflammatory pathways. Furthermore, better identification of intracellular pathways that lead to degradation of tau aggregates in microglia is required. This could help explain why microglia in tauopathies are mostly senescent, inefficient in clearing extracellular tau, and potentially become involved in spreading of tau pathology. The loss of the ability of microglia to keep the extracellular space clean of aggregated proteins may play a critical role in the propagation of protein pathology in the brain.Finally, the role of microglia in the mechanism of action of tau immunotherapy needs to be explored further. Important topics include a better understanding of the fate of tau-antibody complexes in the extracellular space and the associated roles of various antibody isotypes; a better understanding of microglia-mediated clearance mechanisms and other potential clearance pathways like the glymphatic system; and a better characterization of the downstream consequences of Fc-mediated tau antibody internalization. Pre-clinical studies should also report more on the immunological consequences, beyond the mere presence of microgliosis or astrogliosis. Examples would include measuring secreted immune molecules  and identifying effects on transcriptional phenotypes in glia, such as the recently identified disease-associated microglia and neurotoxic A1 astrocytes , 188. Th


Rhythmically bedded cherts are observed in both pelagic marine and lacustrine deposits, but the formation mechanism in the latter remains highly uncertain. Our study of alternating chert–dolomite beds in the Eocene Green River Formation, Utah, USA reveals dense accumulations of organic-matter spheres (30–50 μm diameter) of probable algal cyst origin in the chert layers, and centennial- to millennial-scale periodicities in chert layer deposition. A positive correlation between the degree of degradation of the organic spheres and Si distribution implies decomposition of algal organic matter lead to precipitation of lacustrine chert. As both alkalinity and dissolved silica were likely high in the palaeo-lake waters of the Green River Formation, we hypothesize that decomposition of algal organic matter lowered the pH of sediment pore waters and caused silica precipitation. We propose a formation model in which the initial abundance of algal organic matter in sediment varies with productivity at the lake surface, and the decomposition of this algal matter controls the extent of silica precipitation in sediment. The formation of rhythmically bedded chert–dolomite may be linked to centennial- to millennial-scale climatic/environmental factors that modulate algal productivity, which are possibly tied to solar activity cycles known to have similar periodicities. Bedded cherts exhibiting periodicity are also more rarely found in lacustrine deposits4; but due to the absence (or lack of preservation) of biogenic siliceous remains in pre-Neogene lacustrine chert, the formation mechanism of such bedded cherts remains far more uncertain.Rhythmically alternating beds of chert and shale, known as bedded chert, commonly occur in marine sedimentary rock of pelagic origin. Bedded chert in marine deposits consists mainly of biogenic silica, which originates from siliceous remains of radiolarians, sponges, and diatoms. Changes in the bed thickness of chert are interpreted to represent orbitally paced variations in marine productivity6. It is also noteworthy that lacustrine cherts occur bedded with either trona formed in an evaporative environment4 or with dolomite formed in a shallow saline-lake environment8. Upper Pleistocene lacustrine chert–trona deposits exposed around the highly alkaline Lake Magadi in the East African rift valley12 are considered the prime example of the first type, and similar deposits (referred to as Magadi-type cherts) have been reported from several other localities worldwide15. Previous studies concluded that dilution of alkaline brines by fresh-water input could decrease the pH of the lake water and result in precipitation of magadiite (NaSi7O13(OH)3·3H2O), which probably converted initially to kenyaite (NaSi11O20.5(OH)4·3H2O) and eventually to chert (6SiO2·H2O) by interaction with percolating waters. This inorganic precipitation process has been suggested for the lacustrine cherts in Lake Magadi3, but an alternative organically moderated precipitation mechanism has been suggested in a later study17 as described below.Given the higher solubility of silica in alkaline waters with pH > 9, any process that causes variations in lake-water pH has the potential to be a major controlling factor in silica precipitation18. Collinson7 reported thinly bedded chert, consisting of microcrystalline silica within micritic dolomite in middle Proterozoic strata of eastern North Greenland. The cherts were interpreted as having resulted from the precipitation of primary silica gels in response to the evaporative concentration of silica dissolved in groundwater. Wells14 reported nodular chert within the carbonate deposits of the Paleocene–Eocene Flagstaff Formation in northern Utah, USA, and also suggested that the cause of the initial silica precipitation was evaporative concentration. Buchheim18 reported the occurrence of chert nodules within dolomite beds in the Eocene Green River Formation, west-central USA, which formed in a shallow, hypersaline lake environment. Owen et al.19 observed spring-vent, pedogenic and shallow-marsh cherts close to fossil springs in the Kenya Rift. Many of these studies concluded that lacustrine chert is inorganic in origin, linked to the evaporative concentration of silica and/or subsequent precipitation by changes in the pH of the lake water4.Alternating beds of chert and dolomite have also been reported from lacustrine deposits14. Well-preserved biogenic materials  have been reported in lacustrine chert from the Green River Formation, USA20; the Paleogene succession of the Madrid Basin, Spain8; and Pleistocene deposits in Africa22. However, the potential role of the biogenic material and processes in the formation of lacustrine chert was not fully evaluated in previous studies.It remains intriguing, however, that fossils and biogenic textures are preserved in lacustrine chert16 described evidence for calcareous bioherm and coccoid cyanobacteria structures in chert from Lake Magadi. They suggested that purely inorganic chert is rare in Lake Magadi, and instead proposed that the metabolic processes of cyanobacteria modify the pH of the pore water and influence silica precipitation. Hesse4 also documented several possible mechanisms of biogenic influence on silica precipitation, including production of CO2 by biogenic respiration in lake water or decomposition of organic matter that could result in lowering of the pH and dissolution of calcite and precipitation of silica. Although these studies describe potential linkages between lacustrine chert formation and biogenic activity, the mechanism by which biogenic activity results in the precipitation of silica still remains unclear. Specifically, clear evidence of the biological activity that produced CO2 and pH changes to drive silica precipitation have yet to be demonstrated.A few studies have suggested a potential link between lacustrine chert formation and biogenic activity. Behr and RöhrichtHere we present field observations and geochemical evidence from the Eocene Green River Formation in northern Utah, USA, that indicate deposition of organic matter and its decomposition might play a key role in the formation of lacustrine chert. We find dense accumulations of spherical organic materials of probable algal origin in chert beds, and infer that decomposition of this organic material drove silica precipitation by decreasing the pH of pore waters in bottom sediments. We also discuss the possibility that changes in algal productivity of the lake gave rise to the periodicity observed in lacustrine bedded chert.25. We examined the lacustrine bedded chert succession in the upper part of the formation in the Indian Canyon section, western Uinta Basin  paleoenvironment33. Based on this evidence, the chert–dolomite deposits are interpreted to have been deposited in a highly alkaline and saline-lake palaeoenvironment. Given the occurrence of evaporitic minerals , cherts in the Green River formation have been identified as Magadi-type chert and attributed to an inorganic evaporative origin35. However, in light of the contrary ideas put forward by Behr and Röhricht16, we sought observational and geochemical evidence that would help evaluate if chert formation was related to the deposition and decomposition of organic matter.Following the stratigraphic framework of previous studiesges Fig. . Cherts ges Fig. . The occges Fig. . Microsc36; these spheres have the characteristics of organic matter of algal origin, and a morphology resembling the green algae Botryococcus braunii38 or chrysophytes39. Biomarker analyses further suggest a higher contribution of lacustrine algae and bacteria in the chert layers  in the chert layers Fig. . These iTo clarify the relationship between organic sphere occurrence, degradation degrees, and Si concentration, we undertook elemental mapping by scanning X-ray analytical microscope (SXAM) Fig. . The hig2 comprises about 90% of the chert samples, CaO about 3%, and Al2O3 < 0.01%, a finding that indicates alumino-silicates are not a major contributor to Si in the chert.In addition to periodicities corresponding to thicknesses of ca. 7–9 and 17–20 cm in the chert layers  have been found in the Green River Formation, Si precipitation by such organisms is unlikely. The size and morphology of observed organic spheres are also quite different from lacustrine diatoms of Middle Eocene age reported in Canada45 and Upper Cretaceous age in Mexico46. Instead, the presence of abundant organic spheres in chert layers implies that deposition of algal organic matter was integral to formation of lacustrine chert. Biomarker evidence also supports the formation of chert layers by algal organic matter influence . For the Green River formation, we have shown that significant organic matter is present and that the degree of organic matter decomposition in bottom sediment is spatially and temporally closely tied to the formation of lacustrine bedded chert. Future studies will have to evaluate if this formation mechanism can be successfully applied to other chert deposits that preserve biogenic structures48.In contrast to our model, most previous studies have attributed the formation of lacustrine chert to inorganic processes and evaporative precipitation in a shallow-lake environment49. Owen et al.49 reported siliceous rhizoliths in Pleistocene deposits in Kenya that were possibly formed by plant-root decomposition and the resulting lowering of pH, with the deposited silica sourced from plant opal. Buatois et al.22 described the siliceous ichnofossil Vagorichnus in the sub-lacustrine hydrothermal deposits of Lake Baringo, central Kenya, where they interpreted silica precipitation to have occurred as a result of the interplay between the decomposition of organic matter and dissolved silica sourced from hydrothermal deposits.A similar model of biogenically induced silica precipitation has been suggested in studies of pedogenic rhizoliths and ichnofossils50. Therefore, solar activity cycles, which are known to influence climatic change51, appear to be implicated as a control on the centennial- to millennial-scale changes in algal productivity, although further investigation is required to test this hypothesis.The causal mechanism underlying the periodic alternations of chert and dolomite also needs further study. If lacustrine bedded chert is formed by biogenically induced decomposition of algal organic matter, as is proposed in this study, what process accounts for the apparent periodicity of chert deposition? From the field investigations and elemental mapping analysis, alternating beds of chert and dolomite exhibit periodicities in thickness of ca. 1.0–1.2, 2.2–3.0, 7–9, and 17–20 cm  in the Nagoya University Museum  hydrocarbon, aromatic hydrocarbon and polar compound aliquots. The saturated fractions were further analysed using a Thermo Trace 1310 gas chromatograph coupled to a Thermo TSQ8000 mass spectrometer at University of Southampton.Source input and paleodepositional conditions were interpreted based on the molecular composition of four chert samplesSupplementary Information


Neurodegenerative diseases are incurable and inexorably progressive conditions that affect the central nervous system and result in a selective pattern of neuronal death. Parkinson's disease (PD) and Alzheimer's disease (AD) are the most common neurodegenerative diseases. While most cases are idiopathic, studies have confirmed that genetic factors contribute to the pathogenesis of both PD and AD. PD is characterized by loss of dopamine (DA)-producing neurons of the substantia nigra, and as a consequence of a reduction in striatal DA content. A neuropathological hallmark is the presence of Lewy body inclusions in many of the remaining neurons and Lewy-neurite pathology in the neuropil. The classic histopathological hallmarks of AD are the extracellular accumulation of amyloid-β (Aβ) plaques and intracellular deposition of hyperphosphorylated tau into neurofibrillary tangles. Despite distinct clinical and pathological features, the formation of misfolded protein aggregates is a common feature of neurodegenerative diseases, which can be mainly classified into synucleinopathies, tauopathies, and amyloidopathies. Neurodegenerative diseases share critical processes, such as mitochondrial anomalies, oxidative damage, and inflammation that are implicated in the gradual loss of neuronal function and cell death.Quartey et al.). Furthermore, perturbations in mitochondrial dynamics, mitochondrial transport within axons, mitophagy, and accumulation of somatic mtDNA mutations are associated with impaired mitochondrial function. Compromised mitochondrial quality control mechanisms may lead to the accumulation of defective mitochondria and concomitant oxidative damage, defective calcium (Ca2+) homeostasis and signaling, synaptic pathology, and ferroptotic neuronal death. The present Research Topic aims to critically evaluate the current literature on molecular mechanisms associated with neurodegenerative diseases and it provides novel insights into disturbances in mitochondrial function, which occur during neurodegeneration. This topic also suggests that the development of novel mitochondria-targeted therapeutic strategies may be useful in the treatment of neurodegenerative diseases.A plethora of reports indicate that mitochondrial dysfunction is a central factor in the pathophysiology of neurodegenerative diseases . Axonal transport, a cellular mechanism responsible for the active trafficking of lipids, proteins, neurotransmitters, and organelles, is essential for neuronal network function and viability. Anterograde transport carries new synthesized material from the cell body to distal axons and is mediated by kinesin motor proteins. Dynein-driven retrograde transport is required for efficient distribution of cargoes from the axon terminals toward the soma. Mitochondrial movement along both microtubule and actin filaments is regulated by a motor adaptor complex that attaches the anterograde kinesin-1 motor and retrograde dynein motor to the outer mitochondrial membrane, in a process mediated by the membrane-anchored Miro (RhoT1/2) and Milton (Trak1/2) proteins . There is growing evidence of a crosstalk between fusion-fission and axonal flux mitochondrial dynamics and axonal transport integrity .Mechanisms for the maintenance of mitochondrial integrity and functionality are crucial for neuronal survival. Mitochondrial dynamics play a key role in ensuring mitochondrial quality control and are tightly regulated by the fusion/fission machinery, which allows the formation or degradation of a mitochondrial syncytium. The molecular process of fusion is driven by the GTPases Opa1 and Mitofusin-1 (Mfn1) and Mfn2 while dynamin-related protein (Drp1) interacts with the mitochondrial fission 1 protein (Fis1), mitochondrial fission factor (Mff) and mitochondrial dynamics proteins of 49 and 51 kDa (MiD49/51) to mediate mitochondrial fission.It has been recently shown that mitofilin (Mic60), a component of the MICOS complex that plays a key role in the maintenance of mitochondrial structure and function,can regulate mitochondrial dynamics . Protein post-translational modifications such as enzymatic glycosylation and non-enzymatic glycation together with a disruption of the mitochondrial quality control system, result in defective mitophagy and excessive accumulation of dysfunctional proteins . Altered autophagy phenotypes have recently been associated with optineurin, a multifunctional cargo adaptor protein observed in diverse brain regions of rats after exposure to rotenone . Mitochondria contribute to aging, mitochondrial-related diseases, and neurodegeneration through the accumulation of somatic mtDNA mutations—point mutations and large-scale deletions . Point mutations are likely to arise from an inefficient base excision repair system while mtDNA deletions and rearrangements may result from errors in replication and/or double-strand break repair  into the mitochondrial inner membrane via the Tim/Tom complex plays a pivotal role in regulating Pink1/Parkin-mediated mitophagy . Patients suffering from depression show reduced glucose metabolism in different regions of the brain  in these mice restored cognitive function and attenuated hippocampal neuronal degeneration. Elevated Ca2+ influx plays a key role in promoting pathological tau phosphorylation via modulation of Ca2+-binding proteins and/or dysregulation of the enzymatic activity of kinases and phosphatases , results in the overactivation of the N-methyl-D-aspartate (NMDA) receptors and the subsequent loss of ionic homeostasis and excessive influx of CaAbdalkader et al.). Although pathologically-related aggregate species of α-syn, Aβ and tau regulate lipid peroxidation, glutathione levels, and iron homeostasis, as yet no studies have explored their potential role in ferroptotic cell death.Two main pathways cell death have been distinguished, namely apoptosis (programmed cell death) and necrosis . Ferroptosis, a term coined in 2012, is a form of regulated cell death induced by erastin which is characterized by the iron-dependent accumulation of lipid hydroperoxides with a genetic, morphological, and biochemical profile different from apoptosis and necrosis (Dixon et al., In conclusion, this special issue provides scientists and clinicians with new insights into the molecular mechanisms underlying the role of mitochondrial dysfunction in the pathophysiology of neurodegenerative diseases such as PD and AD. Furthermore, it may provide further rationale for the development of effective therapeutic interventions targeting mitochondria to treat these devastating illnesses.VT confirms being the sole contributor of this work and has approved it for publication.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


RL13 arise quickly, while mutations in the UL128-131A locus emerge later during fibroblast passage and disrupt formation of a glycoprotein complex that is important for entry into epithelial and endothelial cells. As CMV replicates in the context of host antibodies in vivo, we reasoned that antibodies might mitigate the accumulation of adaptive mutations during cell culture passage. To test this, CMV in infant urine was used to infect replicate fibroblast cultures. One lineage was passaged in the absence of CMV-hyperimmuneglobulin (HIG) while the other was passaged with HIG in the culture medium. The former lost epithelial tropism and acquired mutations disrupting RL13 and UL131A expression, whereas the latter retained epithelial tropism and both gene loci remained intact after 22 passages. Additional mutations resulting in single amino acid changes also occurred in UL100 encoding glycoprotein M, UL102 encoding a subunit of the helicase/primase complex, and UL122 encoding the Immediate Early 2 protein. An epitheliotropic RL13+/UL131A+ virus was isolated by limiting dilution in the presence of HIG and expanded to produce a working stock sufficient to conduct cell tropism experiments. Thus, production of virus stocks by culture in the presence of antibodies may facilitate in vitro experiments using viruses that are genetically more authentic than previously available.Propagation of human cytomegalovirus (CMV) in cultured cells results in genetic adaptations that confer improved growth in vitro and significant attenuation in vivo. Mutations in  Human cytomegalovirus (CMV) causes a spectrum of diseases in immune-compromised patients, including retinitis in human immunodeficiency virus patients, pneumonitis in transplant patients, and serious birth defects characterized by sensorineural hearing loss and severe mental retardation when acquired during pregnancy. Available options for treating CMV infections are limited, and are hampered by dose-limiting toxicities and the development of resistance. These therapeutic limitations have fostered continued efforts toward the development of effective vaccines, the identification and exploitation of novel targets for antiviral interventions, and the development of passive polyclonal or monoclonal antibody therapeutics.Since CMV was first isolated in 1957 from clinical samples using cultured human fibroblasts , t, t11], t4–105 pfu/mL), but were sufficient for use in experiments that do not require high multiplicities of infection. For example, we were able to use Ig-KG-H2 to evaluate CMV tropism for N/TERT-1 cells  and to assess the impact of differentiation on infection efficiency , or new BACs could be derived from RL13+ CMV clinical isolates following limited culture in the presence of antibodies. Targeted mutations could then be introduced using E. coli genetics and the resulting mutant viruses reconstituted by transfection of fibroblasts in the presence of antibodies. Mutations in non-essential genes could also be directly engineered in RL13+ viruses grown in the presence of HIG using CRISPR/Cas9 without the need for BAC cloning. Studies of this nature should help to elucidate the mechanisms underlying the repressive role(s) played by RL13 during CMV replication in established cell culture systems such as fibroblasts or ARPE-19 cells, and may prove crucial for identifying augmenting or even essential roles for RL13 in other cell types or in vivo. The culture conditions described here should be useful to extend current CMV genetic systems for evaluation of CMV mutants by allowing for maintenance of an