Miracle-dz/UniFAR-FTUs huggingface dataset:
Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila

ABSTRACT The acquisition of cellular identity during development depends on precise spatiotemporal regulation of gene expression, with combinatorial interactions between transcription factors, accessory proteins and the basal transcription machinery together translating complex signaling inputs into appropriate gene expression outputs. The opposing repressive and activating inputs of the Drosophila ETS family transcription factors Yan and Pointed orchestrate numerous cell fate transitions downstream of receptor tyrosine kinase signaling, providing one of the premier systems for studying this process. Current models describe the differentiative transition as a switch from Yan-mediated repression to Pointed-mediated activation of common target genes. We describe here a new layer of regulation whereby Yan and Pointed co-occupy regulatory elements to repress gene expression in a coordinated manner, with Pointed being unexpectedly required for the genome-wide occupancy of both Yan and the co-repressor Groucho. Using even skipped as a test-case, synergistic genetic interactions between Pointed, Groucho, Yan and components of the RNA polymerase II pausing machinery suggest that Pointed integrates multiple scales of repressive regulation to confer robustness. We speculate that this mechanism may be used broadly to fine-tune the expression of many genes crucial for development. Summary: Recruitment of the transcriptional repressor Yan and the co-repressor Groucho by the transcriptional activator Pointed confers precision and robustness to the gene expression dynamics that drive developmental cell fate transitions.
Cytoplasmic RNA Granules in Somatic Maintenance

Cytoplasmic RNA granules represent subcellular compartments that are enriched in protein-bound RNA species. RNA granules are produced by evolutionary divergent eukaryotes, including yeast, mammals, and plants. The functions of cytoplasmic RNA granules differ widely. They are dictated by the cell type and physiological state, which in turn is determined by intrinsic cell properties and environmental factors. RNA granules provide diverse cellular functions. However, all of the granules contribute to aspects of RNA metabolism. This is exemplified by transcription, RNA storage, silencing, and degradation, as well as mRNP remodeling and regulated translation. Several forms of cytoplasmic mRNA granules are linked to normal physiological processes. For instance, they may coordinate protein synthesis and thereby serve as posttranscriptional “operons”. RNA granules also participate in cytoplasmic mRNA trafficking, a process particularly well understood for neurons. Many forms of RNA granules support the preservation of somatic cell performance under normal and stress conditions. On the other hand, severe insults or disease can cause the formation and persistence of RNA granules that contribute to cellular dysfunction, especially in the nervous system. Neurodegeneration and many other diseases linked to RNA granules are associated with aging. Nevertheless, information related to the impact of aging on the various types of RNA granules is presently very limited. This review concentrates on cytoplasmic RNA granules and their role in somatic cell maintenance. We summarize the current knowledge on different types of RNA granules in the cytoplasm, their assembly and function under normal, stress, or disease conditions. Specifically, we discuss processing bodies, neuronal granules, stress granules, and other less characterized cytoplasmic RNA granules. Our focus is primarily on mammalian and yeast models, because they have been critical to unravel the physiological role of various RNA granules. RNA granules in plants and pathogens are briefly described. We conclude our viewpoint by summarizing the emerging concepts for RNA granule biology and the open questions that need to be addressed in future studies.
Total MRI Small Vessel Disease Burden Correlates with Cognitive Performance, Cortical Atrophy, and Network Measures in a Memory Clinic Population.

BACKGROUND Recent evidence suggests that combining individual imaging markers of cerebral small vessel disease (SVD) may more accurately reflect its overall burden and better correlate with clinical measures. OBJECTIVE We wished to establish the clinical relevance of the total SVD score in a memory clinic population by investigating the association with SVD score and cognitive performance, cortical atrophy, and structural network measures, after adjusting for amyloid-β burden. METHODS We included 243 patients with amnestic mild cognitive impairment (MCI), Alzheimer's disease dementia, subcortical vascular MCI, or subcortical vascular dementia. All underwent MR and [11C] PiB-PET scanning and had standardized cognitive testing. Multiple linear regression was used to evaluate the relationships between SVD score and cognition, cortical thickness, and structural network measures. Path analyses were performed to evaluate whether network disruption mediates the effects of SVD score on cortical thickness and cognition. RESULTS Total SVD score was associated with the performance of frontal (β - 4.31, SE 2.09, p = 0.040) and visuospatial (β - 0.95, SE 0.44, p = 0.032) tasks, and with reduced cortical thickness in widespread brain regions. Total SVD score was negatively correlated with nodal efficiency, as well as changes in brain network organization, with evidence of reduced integration and increasing segregation. Path analyses showed that the associations between SVD score and frontal and visuospatial scores were partially mediated by decreases in their corresponding nodal efficiency and cortical thickness. CONCLUSION Total SVD burden has clinical relevance in a memory clinic population and correlates with cognition, and cortical atrophy, as well as structural network disruption.
Efficient parallel testing: A configurable and scalable broadcast network design using IJTAG

To meet high performance requirements, System-on-Chips (SoCs) may include multiple replicated copies of functional embedded cores. To reduce the time required to apply identical test data to these replicated cores, we designed a novel broadcast network architecture that harnesses IEEE Std 1687 (IJTAG). Our architecture provides highly configurable broadcast/multicast and daisy modes, allowing one to selectively apply test data to any combination of embedded modules. The broadcast network is also scalable, supports hierarchical network architectures, and can be easily interfaced with other IJTAG-compliant test architectures. The new broadcast network provides a trade-off between network reconfigurability and the programming overhead of the network reconfiguration bits. It saves up to 70–80% of the test time in a sample test data broadcast scenario compared to serial and prior broadcast IJTAG networks. Compared to a serial network, our broadcast network requires only one extra reconfiguration bit.
Chapter 2 Fundamentals of Epithelial Na + Absorption

The maintenance of electrolyte balance is essential for the control of many functions in the human body. Na, K, and Cl are key electrolytes that contribute to a variety of processes ranging from the maintenance of cellular membrane potential to the regulation of cell volume and extracellular fluid volume. Fundamentals of epithelial Cl and K transport are discussed in the preceding and following chapters and will be only briefly touched upon here. Na absorption occurs across the epithelial barriers of many organs, including the lung, gastrointestinal tract, exocrine glands, and kidney. Na is the primary determinant of blood volume, and a number of physiological mechanisms that control blood pressure mediate their effects by adjusting Na balance in the kidney. This chapter describes classical fundamentals of epithelial Na absorption and highlights some recent mechanisms involved in physiological regulation of Na transport in specific epithelia with a particular emphasis on the kidney.
Comparing Gefitinib and Erlotinib With Regard To Brain Metastases Recurrence in EGFR-Mutant Non-Small Cell Lung Cancer Patients

Brain metastases of lung cancer are associated with a poor prognosis. Little research has been conducted to directly compare erlotinib with gefitinib regarding the frequency of central nerve system recurrence. This is the first study to directly compare erlotinib with gefitinib in terms of brain metastases recurrence rates in patients with EGFR-mutant NSCLC who had no brain metastasis at the time of starting TKI treatment. This was a single-center retrospective study. Advanced or recurrent non-small cell lung cancer patients with no brain metastases at the time of starting initial tyrosine kinase inhibitor treatment who received either gefitinib or erlotinib monotherapy were selected. The primary endpoint was the incidence of brain metastases, and secondary endpoints included the objective response rate, progression-free survival, overall survival, and Post-Progression Survival in subgroups based on tyrosine kinase inhibitor treatment and the occurrence of brain metastases. There were 119 patients in the gefitinib group and 13 patients in the erlotinib group. Brain metastases at disease progression were observed in 16 patients in the gefitinib group, and in no patients in the erlotinib group (13.5% vs. 0%, p=0.37). The median overall survival was 29.2 months in the gefitinib group and was not reached in the erlotinib group (p=0.14). The median PPS was 15.5 months in the gefitinib group and 23.7 months in the erlotinib group (p=0.11). Based on the occurrence of brain metastases, Post-Progression Survival was significantly longer in the no brain metastases group (8.0 months vs. 17.9 months, p=0.01). These data showed the possibility of a lower central-nerve-system recurrence rate with erlotinib compared with gefitinib. Post-Progression Survival in patients with brain metastases was significantly shorter than that of patients without brain metastases.
Cytoplasmic Polyadenylation Element-Binding Protein Regulates Neurotrophin-3-Dependent β-Catenin mRNA Translation in Developing Hippocampal Neurons

Neuronal morphogenesis, the growth and arborization of neuronal processes, is an essential component of brain development. Two important but seemingly disparate components regulating neuronal morphology have previously been described. In the hippocampus, neurotrophins, particularly brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT3), act to enhance cell growth and branching, while activity-induced branching was shown to be dependent upon intracellular β-catenin. We now describe a molecular link between NT3 stimulation and β-catenin increase in developing neurons and demonstrate that this process is required for the NT3-mediated increase in process branching. Here, we show that β-catenin is rapidly increased specifically in growth cones following NT3 stimulation. This increase in β-catenin is protein synthesis dependent and requires the activity of cytoplasmic polyadenylation element-binding protein-1 (CPEB1), an mRNA-binding protein that regulates mRNA translation. We find that CPEB1 protein binds β-catenin mRNA in a CPE-dependent manner and that both localize to growth cones of developing hippocampal neurons. Both the NT3-mediated rapid increase in β-catenin and process branching are abolished when CPEB1 function is inhibited. In addition, the NT3-mediated increase in β-catenin in growth cones is dependent upon internal calcium and the activity of CaMKII (calcium/calmodulin-dependent kinase II). Together, these results suggest that CPEB1 regulates β-catenin synthesis in neurons and may contribute to neuronal morphogenesis.
Resisting Adversarial Attacks using Gaussian Mixture Variational Autoencoders

Susceptibility of deep neural networks to adversarial attacks poses a major theoretical and practical challenge. All efforts to harden classifiers against such attacks have seen limited success till now. Two distinct categories of samples against which deep neural networks are vulnerable, “adversarial samples” and “fooling samples”, have been tackled separately so far due to the difficulty posed when considered together. In this work, we show how one can defend against them both under a unified framework. Our model has the form of a variational autoencoder with a Gaussian mixture prior on the latent variable, such that each mixture component corresponds to a single class. We show how selective classification can be performed using this model, thereby causing the adversarial objective to entail a conflict. The proposed method leads to the rejection of adversarial samples instead of misclassification, while maintaining high precision and recall on test data. It also inherently provides a way of learning a selective classifier in a semi-supervised scenario, which can similarly resist adversarial attacks. We further show how one can reclassify the detected adversarial samples by iterative optimization.1
Teach your parents and providers well: Call for refocus on the health of trans and gender-diverse children.

Since the mid-20th century, children’s gender diversity[*][1] has been treated as a matter of psychopathology. [1][2]–[3][3] Throughout North America and Europe, children who express their gender in unexpected ways have been compelled to comply with the gender constraints of their particular
What are the Dynamic Effects of Fertilizer Subsidies on Household Well‐being? Evidence from Malawi

This study uses household level panel data from Malawi to measure the contemporaneous and dynamic impacts of fertilizer subsidies on different indicators of household well‐being. Well‐being is measured in this paper using indicators contained in available survey data, such as area cultivated, maize production, asset wealth, respondent‐stated adequacy of food consumption and respondent-stated life satisfaction. The study uses fixed effects and instrumental variable methods to control for endogeneity caused by the non‐random distribution of targeted fertilizer subsidies. Results indicate that the quantity of subsidized fertilizer acquired by a household has a positive contemporaneous effect on area planted, area planted to maize and maize production at the household level. The subsidy also has a significant dynamic effect on the quantity of maize that households produce. Subsidized fertilizer has no significant contemporaneous or dynamic effect on household asset accumulation. Receiving more subsidized fertilizer does not make households feel that their food consumption has been adequate over the past year, but receiving more subsidized fertilizer makes household heads say that they are more satisfied with their lives. Subsidized fertilizer appears to be going to people with more land. In addition, people in villages where members of parliament reside also receive greater quantities of subsidized fertilizer. These findings raise questions about how subsidy recipients are targeted. Improving targeting could increase the positive impacts of fertilizer subsidies on household well‐being.
Isolation and characterization of nitrogen fixing burkholderia Sp.

The bacterium Burkholderia has been isolated from the rhizosphere soils of Mimosa, Lemon, Maize, Sugarcane, Sunflower, Rice, Bhendhi, Sunhemp, Co on and Chilly from the different farms of Tamil Nadu Agricultural University, Coimbatore. Biochemical and physiological characterization was done for the obtained isolates to screen for further studies by using starch hydrolysis, lipid hydrolysis, casein hydrolysis and catalase test, etc. The isolates were checked for their ability to fix nitrogen by using different medium like BMGM and N free BMGM medium. The isolates were also checked for nitrogenase activity by using gas chromatography. B1 and R1 isolates showed high nitrogenase activity (7.99 and 7.15 n moles of ethylene/hr./mg of cell protein respectively). Total genomic DNA was isolated and PCR with 16S rRNA gene specific primers carried out to yields amplicons of 1300 bp size in Burkholderia. The PCR was carried out with specific primers of nifH gene primer for selected isolates. It showed that selected four isolates were found to have nifH gene with 400 bp. The present study revealed that some of the Burkholderia sp. helps in plant growth promoting activities by fixing nitrogen to enhance the yield of crop plants that can be exploited as bioinoculant in agriculture.
Intensive electric arc interaction with polymer surfaces : reorganization of surface morphology and microstructure

Intense electrical arcs were applied to thermoplastic (polyamide 66) and thermoset (fiber reinforced laminated polyester) materials and the resulting carbonization/metallization process was studied on a sub-micron scale with atomic force microscopy to understand very initial stage of reorganization of surface morphology. These changes can be critical in dramatic changes in surface resistivity preceding electric breakthrough. The surface microroughness and the localization of microand nanoparticles at the center (arc initiation area) and along the edges of the samples were significantly different for different arc regimes. We suggested that for thermoset, the material is pulled out of the surface in the arc formation area (the center of sample). Afterwards, the intensive re-deposition occurred along the edges enhancing nonuniform ablation around the arc initiation area. In contrary, for thermoplastic samples, the entire polymer surface was re-melted that resulted in dramatic smoothing of the initially non-uniform surface morphology. q 2005 Elsevier Ltd. All rights reserved.
Thermal conductivity of gases and liquids

The thermal conductivity of gases, liquids, gas mixtures, and liquid solutions is covered. Existing theories and equations proposed for calculation of thermal conductivity at low pressure are reviewed. The thermal conductivity of gases at high pressures, in the critical state and during transition to the liquid state, is discussed. Thermal conductivity equations for nonassociated and associated liquids at atmospheric pressure are cited. Empirical equations were derived for the thermal conductivity of solutions. The basic experimental techniques and theories underlying the experimental methods for determining thermal conductivities of liquids and gases are explained. An analysis of experimental corrections is presented and possible errors of measurement are indicated.
Spinal Trauma in Italy: Actuality and Future Perspectives

According to the current literature, the incidence of spinal trauma with neurological impairment in Italy is estimated to be between 18 and 20 cases per million [1-3]. Usually the most affected patients are young or middle aged, with a male/female ratio of 3,5-4,1 and the trauma is related to road accidents [4-8]. Spine trauma is also related to work accidents: falls from a height in 53% of the cases, road accidents during the drive to and from work in 20% of cases. In the elderly population, the main cause is due to home accidents [4-6]. Spinal Cord Injuries (SCI) are between the main reasons of permanent disability, with a high economic and social expense; their incidence is increasing, due to the different lifestyle and the augmented life expectancy. Primary prevention could reduce the global incidence of spinal cord injuries. Secondary prevention, with a correct diagnosis and treatment in the early phase might reduce the number of negative outcomes, and improve the quality of life of the patients with SCI. A careful clinical and radiological assessment, associated with an early surgical treatment, are of main importance to improve the prognosis of the patient [9,10]. The clinical outcome of SCI patients might be improved in specialized centres, with intensive care unit and specific trauma management protocols.
Prokaryotic assemblages in suspended and subglacial sediments within a glacierized catchment on Qeqertarsuaq (Disko Island), west Greenland

ABSTRACT Microbes transported by glacial meltwater streams are thought to be a product of passive dispersal from both supra‐ and subglacial sources, though studies investigating the origins of these assemblages are scarce. Here, we conducted a survey within a large catchment containing multiple glaciers on Qeqertarsuaq (Disko Island), west Greenland, to investigate whether meltwater‐exported microbial assemblages in suspended sediments differ between glacial meltwater streams, and if they reflect corresponding bulk subglacial and extraglacial sediment communities. Using 16S rRNA gene amplicon sequencing, we found proglacial stream assemblages substantially differ from one another, despite their close spatial proximity. Furthermore, proglacial stream assemblages were composed of greater proportions of Cyanobacteria compared to bulk subglacial sediment communities, dominated by Betaproteobacteria, demonstrating large contributions of meltwater and microbial cells from supraglacial habitats. Corresponding physico‐chemical characteristics of meltwater suggest that streams draining smaller glaciers had more equal contributions of both supra‐ and subglacial inputs compared with the main catchment outlet, aligning with observed changes in assemblage structure, such as the decreased proportion of Cyanobacteria. These results suggest that glacier size and hydrological drainage systems may influence the structure of exported microbial assemblages, and collectively provide insights into their formation and fate in thiscurrent age of deglaciation.
Faithful Inversion of Generative Models for Effective Amortized Inference

Inference amortization methods share information across multiple posterior-inference problems, allowing each to be carried out more efficiently. Generally, they require the inversion of the dependency structure in the generative model, as the modeller must learn a mapping from observations to distributions approximating the posterior. Previous approaches have involved inverting the dependency structure in a heuristic way that fails to capture these dependencies correctly, thereby limiting the achievable accuracy of the resulting approximations. We introduce an algorithm for faithfully, and minimally, inverting the graphical model structure of any generative model. Such inverses have two crucial properties: (a) they do not encode any independence assertions that are absent from the model and; (b) they are local maxima for the number of true independencies encoded. We prove the correctness of our approach and empirically show that the resulting minimally faithful inverses lead to better inference amortization than existing heuristic approaches.