Miracle-dz/UniFAR-FTUs huggingface dataset:
Four Unique Interneuron Populations Reside in Neocortical Layer 1

Sensory perception depends on neocortical computations that contextually adjust sensory signals in different internal and environmental contexts. Neocortical layer 1 (L1) is the main target of cortical and subcortical inputs that provide “top-down” information for context-dependent sensory processing. Although L1 is devoid of excitatory cells, it contains the distal “tuft” dendrites of pyramidal cells (PCs) located in deeper layers. L1 also contains a poorly characterized population of GABAergic interneurons (INs), which regulate the impact that different top-down inputs have on PCs. A poor comprehension of L1 IN subtypes and how they affect PC activity has hampered our understanding of the mechanisms that underlie contextual modulation of sensory processing. We used novel genetic strategies in male and female mice combined with electrophysiological and morphological methods to help resolve differences that were unclear when using only electrophysiological and/or morphological approaches. We discovered that L1 contains four distinct populations of INs, each with a unique molecular profile, morphology, and electrophysiology, including a previously overlooked IN population (named here “canopy cells”) representing 40% of L1 INs. In contrast to what is observed in other layers, most L1 neurons appear to be unique to the layer, highlighting the specialized character of the signal processing that takes place in L1. This new understanding of INs in L1, as well as the application of genetic methods based on the markers described here, will enable investigation of the cellular and circuit mechanisms of top-down processing in L1 with unprecedented detail. SIGNIFICANCE STATEMENT Neocortical layer 1 (L1) is the main target of corticocortical and subcortical projections that mediate top-down or context-dependent sensory perception. However, this unique layer is often referred to as “enigmatic” because its neuronal composition has been difficult to determine. Using a combination of genetic, electrophysiological, and morphological approaches that helped to resolve differences that were unclear when using a single approach, we were able to decipher the neuronal composition of L1. We identified markers that distinguish L1 neurons and found that the layer contains four populations of GABAergic interneurons, each with unique molecular profiles, morphologies, and electrophysiological properties. These findings provide a new framework for studying the circuit mechanisms underlying the processing of top-down inputs in neocortical L1.
Reassessing the role of the Escherichia coli CpxAR system in sensing surface contact

For proper biofilm formation, bacteria must have mechanisms in place to sense adhesion to surfaces. In Escherichia coli, the CpxAR and RcsCDB systems have been reported to sense surfaces. The CpxAR system is widely considered to be responsible for sensing attachment, specifically to hydrophobic surfaces. Here, using both single-cell and population-level analyses, we confirm RcsCDB activation upon surface contact, but find that the CpxAR system is not activated, in contrast to what had earlier been reported. Thus, the role of CpxAR in surface sensing and initiation of biofilm formation should be reconsidered.
Association of physical activity on changes in cognitive function: Boston Puerto Rican Health Study

ABSTRACT Objective: To evaluate the association of habitual physical activity engagement on changes in cognitive function among Puerto Rican adults. Methods: Longitudinal data (2-year follow-up) from the Boston Puerto Rican Health Study were analyzed (n = 862; mean age = 56.5 year). A daily energy expenditure score was calculated using the number of hours over a 24-h period engaged in various activities, including sleeping, light activity, and moderate-to-vigorous exercise. Energy expenditure estimates were weighted based on the rate of oxygen consumption associated with each activity. Seven cognitive function outcomes were evaluated, including an assessment of general cognitive function, episodic memory, attention and working memory, cognitive flexibility, response inhibition, processing speed, and visuo-spatial organization. From these, overall executive function and memory capacity were derived using principal components analysis. Results: Physical activity was not associated with changes in overall executive function. However, compared to those with low baseline physical activity, those with moderate physical activity had 48% reduced odds of having ≥1 standard deviation decline in memory function (OR = 0.52; 95% CI: 0.32, 0.84; p = 0.008) in 2 years. Conclusion: Among Puerto Rican adults, physical activity may help attenuate memory decline.
My life with lupus: contextual responses of African-American women with systemic lupus participating in a peer mentoring intervention to improve disease self-management

Objective The current article seeks to examine the ways in which African-American women with systemic lupus erythematosus (SLE) describe their disease experience and how they cope with their disease. This qualitative study provides deeper insight into whether experiences of African-American women with SLE differ from previous qualitative study findings. Methods Qualitative data were gathered using interviews and a focus group, from participants in the Peer Approaches to Lupus Self-management (PALS) programme. Data were analysed for themes related to disease experience and how participants cope with their disease. Twenty-seven African-American women with SLE were recruited into the peer mentoring programme, of which 7 served as mentors and 20 served as mentees. A 12-week peer mentoring intervention delivered by phone and based on the Chronic Disease Self-Management and Arthritis Self-Management Programs. Results Three categories encompassing a total of 10 subcategories emerged from analyses: (A) interpersonal, familialandromantic relationships; (B) individual experiences of living with SLE; and (C) physician–patient relationships. Conclusion We gained insight on several issues related to patient perspectives of African-American women with SLE, and the context surrounding their thoughts and feelings related to lupus, including their providers, families and other social support networks. Additional research efforts could explore and address the thematic domains and respective subthemes identified here. Although limited due to the preliminary nature of the study, this information can be used to create future evidence-based interventions to decrease the impact of SLE on African-American patients.
The Misgendering Machines

Automatic Gender Recognition (AGR) is a subfield of facial recognition that aims to algorithmically identify the gender of individuals from photographs or videos. In wider society the technology has proposed applications in physical access control, data analytics and advertising. Within academia, it is already used in the field of Human-Computer Interaction (HCI) to analyse social media usage. Given the long-running critiques of HCI for failing to consider and include transgender (trans) perspectives in research, and the potential implications of AGR for trans people if deployed, I sought to understand how AGR and HCI understand the term "gender", and how HCI describes and deploys gender recognition technology. Using a content analysis of papers from both fields, I show that AGR consistently operationalises gender in a trans-exclusive way, and consequently carries disproportionate risk for trans people subject to it. In addition, I use the dearth of discussion of this in HCI papers that apply AGR to discuss how HCI operationalises gender, and the implications that this has for the field's research. I conclude with recommendations for alternatives to AGR, and some ideas for how HCI can work towards a more effective and trans-inclusive treatment of gender.
A General Theory of Equivariant CNNs on Homogeneous Spaces

We present a general theory of Group equivariant Convolutional Neural Networks (G-CNNs) on homogeneous spaces such as Euclidean space and the sphere. Feature maps in these networks represent fields on a homogeneous base space, and layers are equivariant maps between spaces of fields. The theory enables a systematic classification of all existing G-CNNs in terms of their symmetry group, base space, and field type. We also consider a fundamental question: what is the most general kind of equivariant linear map between feature spaces (fields) of given types? Following Mackey, we show that such maps correspond one-to-one with convolutions using equivariant kernels, and characterize the space of such kernels.
Quantitative constraints on autoxidation and dimer formation from direct probing of monoterpene-derived peroxy radical chemistry

Significance Highly oxygenated multifunctional compounds and large-molecular-mass products from the oxidation of forest emissions can drive the formation and growth of atmospheric particles, which contribute significantly to degraded air quality and Earth’s energy balance. Yet, our knowledge of the reaction rates and formation mechanisms of these low-volatility compounds remains poor. Here we provide direct observations of a large suite of organic peroxy radicals (RO2) and related products from O3-initiated oxidation of α-pinene. We observe rapid RO2 autoxidation at room temperature and efficient RO2 cross-reactions forming gaseous dimers (ROOR′), and constrain the role of these processes in secondary organic aerosol mass formation. Our findings shed important light on key monoterpene-derived RO2 chemistry governing particle formation and growth in regions impacted by forest emissions. Organic peroxy radicals (RO2) are key intermediates in the atmospheric degradation of organic matter and fuel combustion, but to date, few direct studies of specific RO2 in complex reaction systems exist, leading to large gaps in our understanding of their fate. We show, using direct, speciated measurements of a suite of RO2 and gas-phase dimers from O3-initiated oxidation of α-pinene, that ∼150 gaseous dimers (C16–20H24–34O4–13) are primarily formed through RO2 cross-reactions, with a typical rate constant of 0.75–2 × 10−12 cm3 molecule−1 s−1 and a lower-limit dimer formation branching ratio of 4%. These findings imply a gaseous dimer yield that varies strongly with nitric oxide (NO) concentrations, of at least 0.2–2.5% by mole (0.5–6.6% by mass) for conditions typical of forested regions with low to moderate anthropogenic influence (i.e., ≤50-parts per trillion NO). Given their very low volatility, the gaseous C16–20 dimers provide a potentially important organic medium for initial particle formation, and alone can explain 5–60% of α-pinene secondary organic aerosol mass yields measured at atmospherically relevant particle mass loadings. The responses of RO2, dimers, and highly oxygenated multifunctional compounds (HOM) to reacted α-pinene concentration and NO imply that an average ∼20% of primary α-pinene RO2 from OH reaction and 10% from ozonolysis autoxidize at 3–10 s−1 and ≥1 s−1, respectively, confirming both oxidation pathways produce HOM efficiently, even at higher NO concentrations typical of urban areas. Thus, gas-phase dimer formation and RO2 autoxidation are ubiquitous sources of low-volatility organic compounds capable of driving atmospheric particle formation and growth.
Analyzing Ethereum's Contract Topology

Ethereum is the second most valuable cryptocurrency today, with a current market cap of over $68B. What sets Ethereum apart from other cryptocurrencies is that it uses the blockchain to not only store a record of transactions, but also smart contracts and a history of calls made to those contracts. Thus, Ethereum represents a new form of distributed system: one where users can implement contracts that can provide functionality such as voting protocols, crowdfunding projects, betting agreements, and many more. However, despite the massive investment, little is known about how contracts in Ethereum are actually created and used. In this paper, we examine how contracts in Ethereum are created, and how users and contracts interact with one another. We modify the geth client to log all such interactions, and find that contracts today are three times more likely to be created by other contracts than they are by users, and that over 60% of contracts have never been interacted with. Additionally, we obtain the bytecode of all contracts and look for similarity; we find that less than 10% of user-created contracts are unique, and less than 1% of contract-created contracts are so. Clustering the contracts based on code similarity reveals even further similarity. These results indicate that there is substantial code re-use in Ethereum, suggesting that bugs in such contracts could have wide-spread impact on the Ethereum user population.
Clinicopathological analysis of oral diffuse large B‐cell lymphoma, NOS: A systematic review

BACKGROUND Diffuse large B-cell lymphoma, NOS (DLBCL NOS) is the commonest extranodal non-Hodgkin lymphoma diagnosed in the oral and maxillofacial region. However, few studies are currently available and its prognostic determinants remain undefined. PURPOSE To analyse the available data on oral DLBCL NOS and to describe its clinicopathological features, identifying potential prognostic factors. METHODS An electronic systematic search was performed using multiple databases with a specific search strategy in April 2018. All reports describing DLBCL NOS involving the oral cavity and jaw bones with sufficient clinicopathological information were assessed. RESULTS Sixty-three publications were included in the study, comprising 122 cases. Oral DLBCL NOS was found predominantly in elderly males (61.5%), and most often presented as an asymptomatic swelling of the gingiva. Patients commonly were HIV-negative (36.1%), with few reports describing EBV-positive cases (four cases/3.3%). Only eight cases presented B symptoms and most cases were classified as stage I or II (48.4%). CHOP therapy was the main treatment option (24.5%) and the overall 5-year survival rate achieved 83%. Males and advanced Ann Arbor stage patients presented significantly lower survival rates in the univariate analysis, but no significance was found in the multivariate model. CONCLUSION Oral DLBCL NOS is an aggressive malignancy, but with a high survival rate.
Multiple prebiotic metals mediate translation

Significance Ribosomes are found in every living organism, where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ∼4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions (low O2, high Fe2+, and high Mn2+). Our results expand the roles of Fe2+ and Mn2+ in ancient and extant biochemistry as cofactors for ribosomal structure and function. Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life’s oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution.
Regional and network properties of white matter function in Parkinson's disease

Parkinson's disease (PD) is a neurodegenerative disorder with dysfunction in cortices as well as white matter (WM) tracts. While the changes to WM structure have been extensively investigated in PD, the nature of the functional changes to WM remains unknown. In this study, the regional activity and functional connectivity of WM were compared between PD patients (n = 57) and matched healthy controls (n = 52), based on multimodel magnetic resonance imaging data sets. By tract‐based spatial statistical analyses of regional activity, patients showed decreased structural‐functional coupling in the left corticospinal tract compared to controls. This tract also displayed abnormally increased functional connectivity within the left post‐central gyrus and left putamen in PD patients. At the network level, the WM functional network showed small‐worldness in both controls and PD patients, yet it was abnormally increased in the latter group. Based on the features of the WM functional connectome, previously un‐evaluated individuals could be classified with fair accuracy (73%) and area under the curve of the receiver operating characteristics (75%). These neuroimaging findings provide direct evidence for WM functional changes in PD, which is crucial to understand the functional role of fiber tracts in the pathology of neural circuits.
The analysis of human leukocyte antigen‐G level in patients with endometrial cancer by Western blot technique

Aberrant expression of human leukocyte antigen‐G (HLA‐G) in various malignancies has been shown to participate in tumour development by suppressing immune regulation within the tumour microenvironment. The detection of HLA‐G has reportedly been correlated with certain clinicopathological parameters in several neoplasms. Both the soluble and membranous forms of HLA‐G are biologically active, and therefore, we aimed to evaluate the HLA‐G level by Western blot technique.
Challenge : Neural Models vs . Templates

E2E NLG Challenge is a shared task on generating restaurant descriptions from sets of key-value pairs. This paper describes the results of our participation in the challenge. We develop a simple, yet effective neural encoder-decoder model 1 which produces fluent restaurant descriptions and outperforms a strong baseline. We further analyze the data provided by the organizers and conclude that the task can also be approached with a template-based model developed in just a few hours.
Clinical and Electrodiagnostic Features Of Nontraumatic Sciatic Neuropathy

Introduction: In this study we sought to characterize etiologies and features of sciatic neuropathy unrelated to penetrating nerve trauma. Methods: This investigation was a retrospective review of 109 patients with electrodiagnostically confirmed sciatic neuropathies. Results: Hip replacement surgery represented the most common (34.9%) etiology, whereas inflammatory sciatic neuropathy was seen in 7.3%. Electrodiagnostic testing revealed an axonal neuropathy in 95.4% and a demyelinating neuropathy in 4.6%. Predominant involvement of the peroneal division was seen in 39.4% and was tibial in 5.5%. Nine of 31 (29.0%) patients who had MRI or neuromuscular ultrasound study showed abnormalities within the sciatic nerve. At the final visit, 46.4% of patients required assistance for ambulation. Young age, lack of severe initial weakness, and presence of tibial compound muscle action potential or sural sensory nerve action potential were predictors of favorable outcome. Discussion: Sciatic neuropathies are usually axonal on electrodiagnostic testing, affect preferentially the peroneal division, and are commonly associated with incomplete recovery. Muscle Nerve 59:309–314, 2019
Multi-source transformer with combined losses for automatic post editing

Recent approaches to the Automatic Post-editing (APE) of Machine Translation (MT) have shown that best results are obtained by neural multi-source models that correct the raw MT output by also considering information from the corresponding source sentence. To this aim, we present for the first time a neural multi-source APE model based on the Transformer architecture. Moreover, we employ sequence-level loss functions in order to avoid exposure bias during training and to be consistent with the automatic evaluation metrics used for the task. These are the main features of our submissions to the WMT 2018 APE shared task, where we participated both in the PBSMT subtask (i.e. the correction of MT outputs from a phrase-based system) and in the NMT subtask (i.e. the correction of neural outputs). In the first subtask, our system improves over the baseline up to -5.3 TER and +8.23 BLEU points ranking second out of 11 submitted runs. In the second one, characterized by the higher quality of the initial translations, we report lower but statistically significant gains (up to -0.38 TER and +0.8 BLEU), ranking first out of 10 submissions.
FlbA-Regulated Gene rpnR Is Involved in Stress Resistance and Impacts Protein Secretion when Aspergillus niger Is Grown on Xylose

Aspergillus niger secretes a large amount and diversity of industrially relevant enzymes into the culture medium. This makes the fungus a widely used industrial cell factory. For instance, carbohydrate-active enzymes of A. niger are used in biofuel production from lignocellulosic feedstock. These enzymes represent a major cost factor in this process. Higher production yields could substantially reduce these costs and therefore contribute to a more sustainable economy and less dependence on fossil fuels. Enzyme secretion is inhibited in A. niger by asexual reproduction. The sporulation protein FlbA is involved in this process by impacting the expression of 36 predicted transcription factor genes. Here, we show that one of these predicted transcriptional regulators, RpnR, regulates protein secretion and proteotoxic stress resistance. The gene is thus an interesting target to improve enzyme production in A. niger. ABSTRACT Proteins are secreted throughout the mycelium of Aspergillus niger except for the sporulating zone. A link between sporulation and repression of protein secretion was underlined by the finding that inactivation of the sporulation gene flbA results in mycelial colonies that secrete proteins throughout the colony. However, ΔflbA strain hyphae also lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 predicted transcription factor genes, one of which, rpnR, was inactivated in this study. Sporulation, biomass, and secretome complexity were not affected in the ΔrpnR deletion strain of the fungus. In contrast, ribosomal subunit expression and protein secretion into the medium were reduced when A. niger was grown on xylose. Moreover, the ΔrpnR strain showed decreased resistance to H2O2 and the proteotoxic stress-inducing agent dithiothreitol. Taking the data together, RpnR is involved in proteotoxic stress resistance and impacts protein secretion when A. niger is grown on xylose. IMPORTANCE Aspergillus niger secretes a large amount and diversity of industrially relevant enzymes into the culture medium. This makes the fungus a widely used industrial cell factory. For instance, carbohydrate-active enzymes of A. niger are used in biofuel production from lignocellulosic feedstock. These enzymes represent a major cost factor in this process. Higher production yields could substantially reduce these costs and therefore contribute to a more sustainable economy and less dependence on fossil fuels. Enzyme secretion is inhibited in A. niger by asexual reproduction. The sporulation protein FlbA is involved in this process by impacting the expression of 36 predicted transcription factor genes. Here, we show that one of these predicted transcriptional regulators, RpnR, regulates protein secretion and proteotoxic stress resistance. The gene is thus an interesting target to improve enzyme production in A. niger.