Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
Capsaicin reactivates hMOF in gastric cancer cells and induces cell growth inhibition

ABSTRACT Capsaicin (CAP) is the major pungent component of chili pepper and is being evaluated for use against numerous types of tumors. Although CAP is indicated to target multiple signaling pathways, exact mechanisms of how it disturb cancer cell metablism remain obscure. Recent studies revealed Sirtuin 1 (SIRT1) serves as a potential target of CAP in cancer cells, indicating a direct regulation of cancer cell histone acetylation by capsaicin. The present study evaluated the effect of CAP on gastric cancer (GC) cell lines to understand the mechanism of cell growth inhibition. The results showed that CAP could significantly suppress cell growth, while altering histone acetylation in GC cell lines. Further studies found that hMOF, a major histone acetyltranferase for H4K16, is central to CAP-induced epigenetic changes. Reduced hMOF activity was detected in GC tissues, which could be restored by CAP both in vivo and in vitro. These findings revealed an important role of hMOF-mediated histone acetylation in CAP-directed anti-cancer processes, and suggested CAP as a potential drug for use in gastric cancer prevention and therapy.
Numerical Simulation of Si Nanosecond Laser Annealing by COMSOL Multiphysics

D transient heat conduction model was created in COMSOL Multiphysics as a simulation of temperature change in material irradiated by KrF beam (248 nm, 27 ns) confined on the silicon's surface (10 - 50 nm). In this paper, the obtained results are shown and discussed in case of bulk Silicon. The heat source is distributed in time with 'gate' and 'gaussian' shapes. The thermal properties values obtained, in case of 'gate' shape, were compared with those obtained in case of 'gaussian' shape. The returned result concerns surface temperature versus time and laser fluence (800-1300 mJ/cm²). Typically, over a laser fluence of 2000 mJ/cm², ablation process occurs on Silicon surface.
Forest bees are replaced in agricultural and urban landscapes by native species with different phenologies and life‐history traits

Anthropogenic landscapes are associated with biodiversity loss and large shifts in species composition and traits. These changes predict the identities of winners and losers of future global change, and also reveal which environmental variables drive a taxon's response to land use change. We explored how the biodiversity of native bee species changes across forested, agricultural, and urban landscapes. We collected bee community data from 36 sites across a 75,000 km2 region, and analyzed bee abundance, species richness, composition, and life‐history traits. Season‐long bee abundance and richness were not detectably different between natural and anthropogenic landscapes, but community phenologies differed strongly, with an early spring peak followed by decline in forests, and a more extended summer season in agricultural and urban habitats. Bee community composition differed significantly between all three land use types, as did phylogenetic composition. Anthropogenic land use had negative effects on the persistence of several life‐history strategies, including early spring flight season and brood parasitism, which may indicate adaptation to conditions in forest habitat. Overall, anthropogenic communities are not diminished subsets of contemporary natural communities. Rather, forest species do not persist in anthropogenic habitats, but are replaced by different native species and phylogenetic lineages preadapted to open habitats. Characterizing compositional and functional differences is crucial for understanding land use as a global change driver across large regional scales.
Role of oxidative stress in the pathophysiology of Toxoplasma gondii infection

Oxidative stress (OS) plays an essential role in the pathogenesis of common neurodegenerative diseases. We have previously shown that Toxoplasma gondii (T. gondii) induces high nitric oxide (NO) production, glial activation, and apoptosis that altogether cause severe neuropathology in toxoplasma encephalitis (TE). The objective of this study was to investigate the cytotoxic effect of OS and to identify a correlation between the causes of T. gondii induced neuropathology. Expression levels of glutathione reductase (GR), Cu/Zn superoxide dismutase (SOD1), neuron specific enolase (NSE), and 8-hydroxy-2’-deoxyguanosine (8-OHdG) were investigated. Results of the study revealed that the levels of GR (P <0.005) and NSE (P <0.001) expression in the brain tissue markedly increased while SOD1 activity decreased (P <0.001) in the infected group compared to the non-infected group. In addition, intense staining for 8-OHdG (P <0.05) was observed both in the nucleus and the cytoplasm of neurons and glial cells that underwent OS. These results were reasonable to suggest that T. gondii-mediated OS might play a pivotal role and a different type of role in the mechanism of neurodegeneration/neuropathology in the process of TE. The results also clearly indicated that increased levels of NO and apoptosis might contribute to OS-related pathogenesis of TE. As a result, OS and expression of NSE might give an idea of the disease progress and may have a critical diagnostic significance for patients with T. gondii infection.
Females drive asymmetrical introgression from rare to common species in Darwin's tree finches

The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger‐bodied C. pauper to the common, smaller‐bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex‐specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species‐specific.
INFLUENCE OF SAMPLE DIRECTION ON THE IMPACT TOUGHNESS OF THE API-X42 MICROALLOYED STEEL WITH A BANDED STRUCTURE VPLIV USMERJENOSTI VZORCEV NA UDARNO @ILAVOST MIKROLEGIRANEGA JEKLA API-X42 S TRAKAVO MIKROSTRUKTURO

The layering of a microstructure parallel to the direction of the material flow during the hot working process is called banding. In the present paper, the severity of ferrite-pearlite banding in the API-X42 microalloyed steel and its effects on the impact energy are studied. Specifically, the impact toughness is examined in the cases of banded and non-banded samples along two directions, perpendicular and parallel to the rolling, and the obtained results are compared. Metallographic examinations, together with the Charpy impact tests at 0 °C and –18 °C, were done for both directions, parallel and perpendicular to the rolling. The results showed a dependence of the impact energy on the sample direction relative to the rolling to be larger with the banded than the non-banded sample. The difference between the impact energies for the directions parallel and perpendicular to the rolling was also noticed to be caused by the increasing anisotropy index.
Metabolite labelling reveals hierarchies in Clostridium acetobutylicum that selectively channel carbons from sugar mixtures towards biofuel precursors

Clostridial fermentation of cellulose and hemicellulose relies on the cellular physiology controlling the metabolism of the cellulosic hexose sugar (glucose) with respect to the hemicellulosic pentose sugars (xylose and arabinose) and the hemicellulosic hexose sugars (galactose and mannose). Here, liquid chromatography–mass spectrometry and stable isotope tracers in Clostridium acetobutylicum were applied to investigate the metabolic hierarchy of glucose relative to the different hemicellulosic sugars towards two important biofuel precursors, acetyl‐coenzyme A and butyryl‐coenzyme A. The findings revealed constitutive metabolic hierarchies in C. acetobutylicum that facilitate (i) selective investment of hemicellulosic pentoses towards ribonucleotide biosynthesis without substantial investment into biofuel production and (ii) selective contribution of hemicellulosic hexoses through the glycolytic pathway towards biofuel precursors. Long‐term isotopic enrichment demonstrated incorporation of both pentose sugars into pentose‐phosphates and ribonucleotides in the presence of glucose. Kinetic labelling data, however, showed that xylose was not routed towards the biofuel precursors but there was minor contribution from arabinose. Glucose hierarchy over the hemicellulosic hexoses was substrate‐dependent. Kinetic labelling of hexose‐phosphates and triose‐phosphates indicated that mannose was assimilated but not galactose. Labelling of both biofuel precursors confirmed this metabolic preference. These results highlight important metabolic considerations in the accounting of clostridial mixed‐sugar utilization.
Neutrophil‐to‐lymphocyte ratio as a bladder cancer biomarker: Assessing prognostic and predictive value in SWOG 8710

Risk stratification is a major challenge in bladder cancer (BC), and a biomarker is needed. Multiple studies have reported the neutrophil‐to‐lymphocyte ratio (NLR) as a promising candidate; however, these analyses have methodological limitations. Therefore, the authors performed a category B biomarker study to test whether NLR is prognostic for overall survival (OS) after curative treatment or is predictive for the survival benefit from neoadjuvant chemotherapy (NAC).
Pharmacological inhibition of mannose-binding lectin ameliorates neurobehavioral dysfunction following experimental traumatic brain injury

Mannose-binding lectin is present in the contusion area of traumatic brain-injured patients and in that of traumatic brain-injured mice, where mannose-binding lectin-C exceeds mannose-binding lectin-A. The reduced susceptibility to traumatic brain injury of mannose-binding lectin double knock-out mice (mannose-binding lectin−/−) when compared to wild type mice suggests that mannose-binding lectin may be a therapeutic target following traumatic brain injury. Here, we evaluated the effects of a multivalent glycomimetic mannose-binding lectin ligand, Polyman9, following traumatic brain injury in mice. In vitro surface plasmon resonance assay indicated that Polyman9 dose-dependently inhibits the binding to immobilized mannose residues of plasma mannose-binding lectin-C selectively over that of mannose-binding lectin-A. Male C57Bl/6 mice underwent sham/controlled cortical impact traumatic brain injury and intravenous treatment with Polyman9/saline. Ex-vivo surface plasmon resonance studies confirmed that Polyman9 effectively reduces the binding of plasma mannose-binding lectin-C to immobilized mannose residues. In vivo studies up to four weeks post injury, showed that Polyman9 induces significant improvement in sensorimotor deficits (by neuroscore and beam walk), promotes neurogenesis (73% increase in doublecortin immunoreactivity), and astrogliosis (28% increase in glial fibrillary acid protein). Polyman9 administration in brain-injured mannose-binding lectin−/− mice had no effect on post-traumatic brain-injured functional deficits, suggestive of the specificity of its neuroprotective effects. The neurobehavioral efficacy of Polyman9 implicates mannose-binding lectin-C as a novel therapeutic target for traumatic brain injury.
Technology as friend or foe? Do electronic health records increase burnout?

Purpose of review To summarize recent relevant studies regarding the use of electronic health records and physician burnout. Recent findings Recently acquired knowledge regarding the relationship between electronic health record use, professional satisfaction, burnout, and desire to leave clinical practice are discussed. Summary Adoption of electronic health records has increased across the United States and worldwide. Although electronic health records have many benefits, there is growing concern about the adverse consequences of their use on physician satisfaction and burnout. Poor usability, incongruent workflows, and the addition of clerical tasks to physician documentation requirements have been previously highlighted as ongoing concerns with electronic health record adoption. In multiple recent studies, electronic health records have been shown to decrease professional satisfaction, increase burnout, and the likelihood that a physician will reduce or leave clinical practice. One interventional study demonstrated a positive effect of a dedicated electronic health record entry clerk on physicians working in an outpatient practice.
Soil Stabilisation Using Sustainable Industrial By-Product Binders and Alkali Activation

This paper presents a laboratory study to assess the performance and feasibility of using various industrial-by-products and alkali activation in stabilising an artificial soft soil. Various geotechnical and mineralogical tests were conducted for curing periods up to 56 days. Comparisons with the performances of non-activated and CEM-I stabilised soils were made. Results indicate that stabilisation using blast furnace slag based binders and alkali activation resulted in the most enhanced engineering performances; whereby alkali activation was seen to initiate pozzolanic reactions and subsequent mechanical property improvements with time, such as strength.
Working Paper : Project on the Next Generation of Teachers Teacher Turnover in High-Poverty Schools : What We Know and Can Do

What fuels high rates of teacher turnover in schools that serve large numbers of low-income students of color? Teachers who choose to leave such schools usually transfer to schools serving wealthier, whiter student populations, leading some researchers to conclude that teachers are dissatisfied working with poor, minority students. Here we present an alternative explanation— one grounded in organizational theory. We review evidence from six recent studies, which collectively suggest that teachers who leave high-poverty schools are not fleeing their students, but rather the poor working conditions that make it difficult for them to teach and their students to learn. Together, these studies find that the working conditions teachers prize most—and those that best predict their satisfaction and retention—are social in nature. They include school leadership, collegial relationships, and elements of school culture. We discuss what is known about these factors and how each supports teachers' work. We conclude with recommendations for those who seek to stabilize the staffing in these schools.
Genetic analysis of chicken egg yolk cholesterol.

Abstract Five yolk traits of White Leghorn eggs were analyzed for heritabilities and genetic correlations in five random bred generations and for response in two generations of selection for low mg. cholesterol/g. dry yolk. The yolk of each egg was weighed and freeze dried after which mg. cholesterol/g. dry yolk was determined. There were 40 sires mated to 600 dams in each generation for three years and 24 sires mated to 360 dams in each of the last two years. Two eggs per hen were used in the first year and the repeatabilities of wet yolk weight, dry yolk weight, yolk moisture weight, mg. cholesterol/g. dry yolk and cholesterol in total yolk were 66.1%, 66.8%, 59.5%, 80.4% and 77.0%, respectively. In the remaining generations one egg per hen was used. Pooled means of five random mated generations and heritabilities from sire variance components, dam components and regressions of daughter on dam, within sires, were: wet yolk weight, 14.52 ± 0.03 g. , 0.26 ± 0.07, 0.44 ± 0.14, 0.22 ± 0.06; dry yolk weight, 7.48 ± 0.02 g. , 0.24 ± 0.07, 0.48 ± 0.14, 0.21 ± 0.06; yolk moisture weight, 7.04 ± 0.02 g. , 0.25 ± 0.07, 0.52 ± 0.14, 0.23 ± 0.06; mg. cholesterol/g. dry yolk, 30.36 ± 0.05 mg. , 0.15 ± 0.05, negative, 0.19 ± 0.06; cholesterol in total yolk, 225.73 ± 0.66 mg. , 0.27 ± 0.07, 0.10 ± 0.14, 0.28 ± 0.05. The correlations between wet yolk wt. , dry yolk wt. and yolk moisture wt. were high (mostly above 0.90), while the genetic correlations between mg. cholesterol/g. dry yolk and the yolk weights were 0.28 to 0.35. There was a high 0.71 to 0.74 genetic correlation between mg. cholesterol/g. dry yolk and cholesterol in total yolk. The realized heritabilities from two replications of two generations of selection ranged from 0.04 to 0.13.
A High-Security Searchable Encryption Framework for Privacy-Critical Cloud Storage Services

Searchable encryption has received a signi cant attention from the research community with various constructions being proposed, each achieving asymptotically optimal complexity for speci c metrics (e.g., search, update). Despite their elegancy, the recent attacks and deployment e orts have shown that the optimal asymptotic complexity might not always imply practical performance, especially if the application demands a high privacy. Hence, there is a signi cant need for searchable encryption frameworks that capture the recent attacks with actual deployments on cloud infrastructures to assess the practicality under realistic settings. In this article, we introduce a new Dynamic Searchable Symmetric Encryption (DSSE) framework called IncidenceMatrix (IM)-DSSE, which achieves a high level of privacy, e cient search/update, and low client storage with actual deployments on real cloud settings. We harness an incidence matrix along with two hash tables to create an encrypted index, on which both search and update operations can be performed e ectively with minimal information leakage. This simple set of data structures surprisingly o ers a high level of DSSE security while at the same time achieving practical performance. Speci cally, IM-DSSE achieves forward privacy, backward privacy and size-obliviousness properties simultaneously. We also create several DSSE variants, each o ering di erent trade-o s (e.g., security, computation) that are suitable for di erent cloud applications and infrastructures. Our framework was fully-implemented and its performance was rigorously evaluated on a real cloud system (Amazon EC2). Our experimental results con rm that IM-DSSE is highly practical even when deployed on mobile phones with a large outsourced dataset. Finally, we have released our IM-DSSE framework as an open-source library for a wide development and adaptation. Keywords— Privacy-enhancing technologies; private cloud services; dynamic searchable symmetric encryption
Sodium and chloride requirements of growing broiler chickens (twenty-one to forty-two days of age) fed corn-soybean diets.

Two trials were conducted to determine Na+ and Cl- nutritional requirements and dietary electrolyte balance (DEB) and its effects on acid-base balance, litter moisture, and incidence of tibial dyschondroplasia (TD) in broiler chickens during the growing period. Cobb broilers were distributed in a completely randomized design (30 pens) with six treatments, five replicates, and 50 birds per experimental unit at 21 d of age. Treatments used in both trials were a basal diet with 0.10% Na+ (Trial 1) or Cl- (Trial 2) supplemented to result in diets with Na+ or Cl- levels of 0.10, 0.15, 0.20, 0.25, 0.30, and 0.35%. In the first trial, the results indicated an optimum Na+ requirement of 0.15%. The Na+ levels, obtained with supplemental NaHCO3, did not affect blood gas parameters and TD incidence. Litter moisture increased linearly with Na+ levels. In the second trial, the Cl- requirement was estimated at 0.23%. Increasing Cl- levels, provided by NaCl with NaHCO3 to balance Na+, caused a linear effect (P < or = 0.01) on blood gas parameters, with an estimated equilibrium at 0.19% dietary Cl-. No effect (P > or = 0.05) of Cl- levels on litter moisture was observed. The hypertrophic area of growth plate in the proximal tibiotarsus increased with Cl- levels (P < or = 0.001). A nonlinear model describes this response. The best dietary electrolyte balance (DEB) was between 250 to 261 mEq/kg in Trial 1 and 249 to 257 mEq/kg in Trial 2. We concluded that the Na+ requirement was 0.15%, and the Cl- requirement was 0.23% for maximum performance of growing chickens between 21 and 42 d of age, and the best DEB was between 249 and 261 mEq/kg.