Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenomics coverage data extraction and aggregation in R with tidyCoverage

Summary The tidyCoverage R package provides a framework for intuitive investigation of collections of genomic tracks over genomic features, relying on the principle of tidy data manipulation. It defines two data structures, CoverageExperiment and AggregatedCoverage classes, directly extending the SummarizedExperiment fundamental class, and introduces a principled approach to exploring genome-wide data. This infrastructure facilitates the extraction and manipulation of genomic coverage track data across individual or multiple sets of thousands of genomic loci. This allows the end user to rapidly visualize track coverage at individual genomic loci or aggregated coverage profiles over sets of genomic loci. tidyCoverage seamlessly combines with the existing Bioconductor ecosystem to accelerate the integration of genome-wide track data in epigenomic analysis workflows. tidyCoverage emerges as a valuable tool, contributing to the advancement of epigenomics research by promoting consistency, reproducibility, and accessibility in data analysis. Availability and implementation tidyCoverage is an R package freely available from Bioconductor ≥ 3.19 (https://www.bioconductor.org/packages/tidyCoverage) for R ≥ 4.4. The software is distributed under the MIT License and is accompanied by example files and data. Contact jacques.serizay@pasteur.fr Supplementary information Additional documentation is available from https://js2264.github. io/tidyCoverage/ and https://js2264.github. io/tidyCoverage/articles/tidyCoverage.html.
Multiplexed Short-wave Infrared Imaging Highlights Anatomical Structures in Mice

While multiplexed fluorescence imaging is frequently used for in vitro microscopy, extending the technique to whole animal imaging in vivo has remained challenging due to the attenuation and scattering of visible and traditional near infrared (NIR-I) wavelengths. Fluorescence imaging using short-wave infrared (SWIR, 1000 – 1700 nm, a.k.a. NIR-II) light enables deeper tissue penetration for preclinical imaging compared to previous methods due to reduced tissue scattering and minimal background autofluorescence in this optical window. Combining NIR-I excitation wavelengths with multiple distinct SWIR emission peaks presents a tremendous opportunity to distinguish multiple fluorophores with high precision for non-invasive, multiplexed anatomical imaging in small animal models. SWIR-emitting semiconductor quantum dots (QDs) with tunable emission peaks and optical stability have emerged as powerful contrast agents, but SWIR imaging demonstrations have yet to move beyond two-color imaging schemes. In this study, we engineered a set of three high quantum yield lead sulfide/cadmium sulfide (PbS/CdS) core/shell QDs with distinct SWIR emissions ranging from 1100 – 1550 nm and utilize these for simultaneous three-color imaging in mice. We first use QDs to non-invasively track lymphatic drainage, highlighting the detailed network of lymphatic vessels with high-resolution with a widefield imaging over a 2 hr period. We then perform multiplexed imaging with all three QDs to distinctly visualize the lymphatic system and spatially overlapping vasculature network. This work establishes optimized SWIR QDs for next-generation multiplexed preclinical imaging, moving beyond the capability of previous dual-labeling techniques. The capacity to discriminate several fluorescent labels through non-invasive NIR-I excitation and SWIR detection unlocks numerous opportunities for studies of disease progression, drug biodistribution, and cell trafficking dynamics in living organisms.
Three ways that non-differentiability affects neural network training

This paper investigates how non-differentiability affects three different aspects of the neural network training process. We first analyze fully connected neural networks with ReLU activations, for which we show that the continuously differentiable neural networks converge faster than non-differentiable neural networks. Next, we analyze the problem of L 1 regularization and show that the solutions produced by deep learning solvers are incorrect and counter-intuitive even for the L 1 penalized linear model. Finally, we analyze the Edge of Stability problem, where we show that all convex, non-smooth, Lipschitz continuous functions display unstable convergence, and provide an example of a result derived using twice differentiable functions which fails in the once differentiable setting. More generally, our results suggest that accounting for the non-linearity of neural networks in the training process is essential for us to develop better algorithms, and to get a better understanding of the training process in general.
Dynamic Susceptibility Contrast Agent Hypoxia-Induced Deoxyhemoglobin as a Cerebrovascular Disease Using Transient Assessing Perfusion in Steno-Occlusive

BACKGROUND AND PURPOSE: Resting brain tissue perfusion in cerebral steno-occlusive vascular disease can be assessed by MR imaging using gadolinium-based susceptibility contrast agents. Recently, transient hypoxia-induced deoxyhemoglobin has been investigated as a noninvasive MR imaging contrast agent. Here we present a comparison of resting perfusion metrics using transient hypoxia-induced deoxyhemoglobin and gadolinium-based contrast agents in patients with known cerebrovascular steno-occlusive disease. MATERIALS AND METHODS: Twelve patients with steno-occlusive disease underwent DSC MR imaging using a standard bolus of gadolinium-based contrast agent compared with transient hypoxia-induced deoxyhemoglobin generated in the lungs using an automated gas blender. A conventional multi-slice 2D gradient echo sequence was used to acquire the perfusion data and analyzed using a standard tracer kinetic model. MTT, relative CBF, and relative CBV maps were generated and compared between contrast agents. RESULTS: The spatial distributions of the perfusion metrics generated with both contrast agents were consistent. Perfusion metrics in GM and WM were not statistically different except for WM MTT. CONCLUSIONS: Cerebral perfusion metrics generated with noninvasive transient hypoxia-induced changes in deoxyhemoglobin are very similar to those generated using a gadolinium-based contrast agent in patients with cerebrovascular steno-occlusive
The Drosophila homolog of MCPH 1 , a human microcephaly gene , is required for genomic stability in the early embryo

The Drosophila homolog of MCPH1, a human microcephaly gene, is required for genomic stability in the early embryoThe Drosophila homolog of MCPH1, a human microcephaly gene, is required for genomic stability in the early embryo" The Drosophila homolog of MCPH1, a human microcephaly gene, is required for genomic stability in the early embryo Introduction Drosophila melanogaster is an ideal model organism for study of the cell cycle during development (reviewed by Foe et al., 1993; Lee and Orr-Weaver, 2003). Drosophila achieves rapid embryogenesis by using a streamlined cell cycle that is not dependent on transcription or growth. The first 13 embryonic cell cycles are nearly synchronous nuclear divisions without cytokinesis occurring in the shared cytoplasm of the syncytial blastoderm. These cycles differ from canonical G1-S-G2-M cycles in that they have no intervening gaps; instead DNA replication and mitosis rapidly oscillate. Maternal RNA and protein stockpiles drive these abbreviated 'S-M' cycles (~10 minutes each). In mammalian embryos, rapid peri-gastrulation divisions that occur later in development share many features and have been proposed to be related by evolutionary descent to early embryonic divisions of flies and frogs (O'Farrell et al., 2004). Thus, advances gained from studies of these streamlined cycles in 'simple' model organisms likely have relevance for understanding mammalian cell cycles. In a genetic screen for regulators of embryonic S-M cycles, we identified the Drosophila homolog of a human disease gene, MCPH1 (microcephalin). Mutation of human MCPH1 causes autosomal recessive primary microcephaly, a developmental disorder characterized by severe reduction of
Improving Efficiency of the Filling Line in a Dairy Industry

⎯ In the dairy manufacturing company the efficiency of the juice filler line is around 53%. We are trying to improve it to around 70% or more. In this project we used the DMAIC methodology for process improvement. Through the first week of data observation a clear tendency is seen throughout the process. Those bottlenecks of the process are the full refrigerator, slow bottles flow and caser mechanism. A cause and effect and pareto charts were developed after a brainstorming with the operators and the mechanics. After those analyses it was found the root causes of the problems. A visual aid by the machines was proposed to increase communication between operator and mechanics. After the implementation the operators, mechanics and internal suppliers should receive continuous training using that new mechanism to report failures. It is also important to keep the process within the specifications to avoid the possibility of muda (waste).
The Effect of Epidural Electrical Stimulation Application in Individuals with Spinal Cord Injury

Spinal cord injury (SCI) is a significant cause of disability, affecting both children and adults worldwide. These injuries can arise from various conditions, including traumatic, vascular, tumor-related, infection-related, inflammatory (such as multiple sclerosis), or neurodegenerative (like motor neuron disease) origins. Among these, traumatic spinal cord injuries caused by reasons like falls and traffic accidents stand out, particularly in developed countries. Epidural electrical stimulation (EES) was initially used to inhibit chronic pain. Subsequent studies have shown its effectiveness in individuals with SCI. In research spanning from the past to the present, EES applications have been utilized for activities such as motor function improvement, sensory enhancement, bowel functions, increased sexual functionality, and regulating heart rhythms in people with SCI. However, the exact impact of EES remains inconclusive at present and is still a subject of debate.
Site-selective protonation enables ef ﬁ cient carbon monoxide electroreduction to acetate

Electrosynthesis of acetate from CO offers the prospect of a low-carbon-intensity route to this valuable chemical –– but only once suf ﬁ cient selectivity, reaction rate and stability are realized. It is a high priority to achieve the protonation of the relevant intermediates in a controlled fashion, and to achieve this while suppressing the competing hydrogen evolution reaction (HER) and while steering multicarbon (C 2+ ) products to a single valuable product –– an example of which is acetate. Here we report interface engineering to achieve solid/liquid/gas triple-phase interface regulation, and we ﬁ nd that it leads to site-selective protonation of intermediates and the preferential stabilization of the ketene intermediates: this, we ﬁ nd, leads to improved selectivity and energy ef ﬁ ciency toward acetate. Once we further tune the catalyst composition and also optimize for interfacial water management, we achieve a cadmium-copper catalyst that shows an acetate Faradaic ef ﬁ ciency (FE) of 75% with ultralow HER (<0.2% H 2 FE) at 150 mA cm − 2 . We develop a high-pressure membrane electrode assembly system to increase CO coverage by controlling gas reactant distribution and achieve 86% acetate FE simultaneous with an acetate full-cell energy ef ﬁ ciency (EE) of 32%, the highest energy ef ﬁ - ciency reported in direct
GHÂNCARAN: JURNAL PENDIDIKAN BAHASA DAN SASTRA INDONESIA

research aim to describe The profiency of logic and creativity in class X anecdotal text material developed in the independent curriculum. The approach and design in this research is qualitative with text analysis as the research objective in the form of content analysis. The results of the study show that the aspects of creativity are accommodated and creativity in learning is related to anecdotal text material in the independent curriculum. Moreover, the exploration of its development is quite explorative by linking anecdotal text material with comedic art that is currently popular, namely stand up comedy.
Intelligent Systems with Applications

Disruptive situations are emotionally-charged events diverging from ordinary behavior, like people ﬁghting or screaming. Public transports are one type of social environment where disruptive situation may occur, and their timely detection may bring signiﬁcant improvements to people’s safety. Current approaches to disruptive situation detection, typically based on CCTVs, do not take the emotional dimension into account. Conversely, we propose to frame such a problem as a speech emotion recognition task. To validate our hypotheses, we carry out an extensive experimental study focusing on the development of a model characterized by speaker/gender independence, robustness to noise, and robustness against multiple voices. We investigate a variety of audio features, classiﬁers, datasets, and data augmentation methods in an eﬀort to deﬁne eﬀective ways to address this under-investigated yet socially signiﬁcant problem. Our experiments show that the proposed systems attain an F1 score of over 90 % on the disruptive class, even when introducing noisy elements such as environmental noise or multiple overlapping voices. This robust performance is achieved with datasets characterized by speaker variability, gender diversity, and varying number of samples. Such promising results indicate that framing disruptive situation detection as a speech emotion recognition task could pave the way to the adoption of new types of intelligent systems with a positive impact on public safety.
Population Variation In and Selection For Resistance to Population Variation In and Selection For Resistance to Pyrethroid-Neonicotinoid Insecticides in the Bed Bug Pyrethroid-Neonicotinoid Insecticides in the Bed Bug

Pyrethroid resistance in bed bugs, Cimexlectularius, has prompted a change to combination products that include a pyrethroid and a neonicotinoid. Ten populations of bed bugs were challenged with two combination products (Temprid SC H and Transport GHP H ). Susceptibility of these populations varied, with the correlated response of the two products indicating cross resistance. We imposed selection on three populations using label rate Temprid, and then reared progeny from unselected and selected strains. All selected strains were significantly less susceptible to Temprid SC than unselected strains. Temprid selected strains were also less susceptible to Transport. The pyrethroid component of Temprid showed asignificantly higher LD 50 in selected strains, but susceptibility to the neonicotinoid remained unchanged. Taken together these results indicate resistance to combination insecticides is present in field populations at levels that should be of concern, and that short-term selection affecting existing variance in susceptibility can quickly increase resistance.
The Effect of High School Matriculation Awards: Evidence from Randomized Trials

In Israel, as in many other countries, a high school matriculation certificate is required by universities and some jobs. In spite of the certificate's value, Israeli society is marked by vast differences in matriculation rates by region and socioeconomic status. We attempted to increase the likelihood of matriculation among low-achieving students by offering substantial cash incentives in two demonstration programs. As a theoretical matter, cash incentives may be helpful if low-achieving students reduce investment in schooling because of high discount rates, part-time work, or face peer pressure not to study. A small pilot program selected individual students within schools for treatment, with treatment status determined by previous test scores and a partially randomized cutoff for low socioeconomic status. In a larger follow-up program, entire schools were randomly selected for treatment and the program operated with the cooperation of principals and teachers. The results suggest the Achievement Awards program that randomized treatment at the school level raised matriculation rates, while the student-based program did not.
Model based assessment of climate change impact on inland flood risk in coastal areas caused by compounding storm tide and precipitation events

In addition to storm surges, inland flooding due to intense rainfall becomes an increasing threat at coastal lowlands. In particular, the coincidence of both types of events poses great challenges to regional water boards since their technical drainage capacities are limited. The evaluation of historical inland flood events at the German North Sea coast at the gauge 10 Knock near Emden shows that in the past mainly moderate storm series in combination with large-scale, heavy precipitation led to an overload of inland drainage systems, whereas storm tides and precipitation alone could be handled well. Evaluation of the drivers of inland flood events simulated for the control period of two climate models confirms that a combination of storm tides and precipitation leads to highest drainage system overloads. Moderate system overload is also caused by heavy precipitation events alone rather than by storm tides without precipitation. Scenario projections based on a set of combinations 15 of two highly resolved climate models and two emission scenarios suggest that the intensity of compound events of rainfall and storm tides will increase consistently against the background of mean sea level rise for all investigated climate change projections, while simulated system overload is higher for RCP8.5 compared to RCP2.6 scenario. Comparable to the past, future compound events will cause more potential damage compared to single extreme events. Such behaviour can be expected to induce an increasing frequency and intensity of inland drainage system overloads along the North Sea coast if timely 20 adaptation measures will not be taken.
Exploring Hardware Fault Impacts on Different Real Number Representations of the Structural Resilience of TCUs in GPUs

The most recent generations of graphics processing units (GPUs) boost the execution of convolutional operations required by machine learning applications by resorting to specialized and efficient in-chip accelerators (Tensor Core Units or TCUs) that operate on matrix multiplication tiles. Unfortunately, modern cutting-edge semiconductor technologies are increasingly prone to hardware defects, and the trend to highly stress TCUs during the execution of safety-critical and high-performance computing (HPC) applications increases the likelihood of TCUs producing different kinds of failures. In fact, the intrinsic resiliency to hardware faults of arithmetic units plays a crucial role in safety-critical applications using GPUs (e.g., in automotive, space, and autonomous robotics). Recently, new arithmetic formats have been proposed, particularly those suited to neural network execution. However, the reliability characterization of TCUs supporting different arithmetic formats was still lacking. In this work, we quantitatively assessed the impact of hardware faults in TCU structures while employing two distinct formats (floating-point and posit) and using two different configurations (16 and 32 bits) to represent real numbers. For the experimental evaluation, we resorted to an architectural description of a TCU core (PyOpenTCU) and performed 120 fault simulation campaigns, injecting around 200,000 faults per campaign and requiring around 32 days of computation. Our results demonstrate that the posit format of TCUs is less affected by faults than the floating-point one (by up to three orders of magnitude for 16 bits and up to twenty orders for 32 bits). We also identified the most sensible fault locations (i.e., those that produce the largest errors), thus paving the way to adopting smart hardening solutions.
The Changing Scale and Configuration of Mesa Verde Communities

ABSTRACT Comparative demographic analyses of nine locations across the Northern San Juan region reveal highly variable population growth rates between A.D. 900 and 1300. We used both fixed and increasing site use life estimates to measure population density and to estimate the size of individual residential communities for the early Pueblo II through late Pueblo III periods. The results reveal that population density increased in the more agriculturally productive central Mesa Verde region but remained stable or declined on its peripheries. Over time, the central Mesa Verde region underwent varied demographic changes, including brief periods of rapid growth; we argue that these brief periods were the result of small-scale, local migrations that reflected shifts in the sociopolitical landscape, rather than concerns with local environmental productivity. Additional analyses of community organization suggests that relatively small and dispersed sites made up an important part of the Mesa Verde region social landscape even after the formation of nucleated villages.
A Novel Method to Construct a Consilience Manifesto

As world events spiral ever more closely to the drain, Phalse Prophets (Post Carbon Institute 2023) will likely be compelled to publish increasingly unhelpful or even dangerous manifestos. Given society’s tendency to champion shallow but over -confident thinkers, it may be time for true scholars to hurl a Hail Mary to gain relevance and head off the worst. An experimental protocol is described that successfully induced in a normally reticent scientist the personality traits that enable outlandish manifesto writing. In contrast to most ideologues, this exercise was done with the prosocial goal of bridging divides and creating consilience. The protocol was a success, but the value of the resulting manifesto is doubtful.
Impact of the Timing of Percutaneous Catheter Drainage Following Endoscopic Drainage on Outcomes in Acute Necrotizing Pancreatitis

Background The role of dual-modality drainage of walled-off necrosis (WON) in patients with acute pancreatitis (AP) is established. However, there are no data on the association of clinical outcomes with the timing of percutaneous catheter drainage (PCD). We investigated the impact of the timing of PCD following endoscopic drainage of WON on clinical outcomes in AP. Materials and Methods This retrospective study comprised consecutive patients with necrotizing AP who underwent endoscopic cystogastrostomy (CG) of WON followed by PCD between September 2018 and March 2023. Based on endoscopic CG to PCD interval, patients were divided into groups (≤ and >3 days, ≤ and >1 week, ≤ and >10 days, and ≤ and >2 weeks). Baseline characteristics and indications of CG and PCD were recorded. Clinical outcomes were compared between the groups, including length of hospitalization, length of intensive care unit stay, need for surgical necrosectomy, and death during hospitalization. Results Thirty patients (mean age ± standard deviation, 35.5 ± 12.7 years) were evaluated. The mean CG to PCD interval was 11.2 ± 7.5 days. There were no significant differences in baseline characteristics and indications of CG and PCD between the groups. The mean pain to CG interval was not significantly different between the groups. Endoscopic necrosectomy was performed in a significantly greater proportion of patients undergoing CG after 10 days (p = 0.003) and after 2 weeks (p = 0.032). There were no significant differences in the complications and clinical outcomes between the groups. Conclusion The timing of PCD following endoscopic CG does not affect clinical outcomes.