Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization

The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess the magnitude of this shock in hybrid yeasts, we investigated the transcriptomic differences between a newly formed Saccharomyces cerevisiae × Saccharomyces uvarum diploid hybrid and its diploid parentals, which diverged ∼20 mya. RNA sequencing (RNA-Seq) based allele-specific expression (ASE) analysis indicated that gene expression changes in the hybrid genome are limited, with only ∼1–2% of genes significantly altering their expression with respect to a non-hybrid context. In comparison, a thermal shock altered six times more genes. Furthermore, differences in the expression between orthologous genes in the two parental species tended to be diminished for the corresponding homeologous genes in the hybrid. Finally, and consistent with the RNA-Seq results, we show a limited impact of hybridization on chromatin accessibility patterns, as assessed with assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Overall, our results suggest a limited genomic shock in a newly formed yeast hybrid, which may explain the high frequency of successful hybridization in these organisms.
Plant‐Mycorrhizal Community Dynamics Associated with a Moisture Gradient within a Rehabilitated Prairie Fen

Wetland ecosystems have ecological significance in areas such as natural waste purification and nutrient cycling. Much has been accomplished in determining the floristic and edaphic characteristics of wetlands, but little is known about key structure‐function relationships such as mycorrhizae. We collected descriptive data on the plant and mycorrhizal fungal community associated with a moisture gradient along a rehabilitated prairie fen to assist in ongoing restoration efforts (Zimmerman Prairie, Greene County, Ohio). Analysis of soil samples from the prairie fen indicated that significant levels of arbuscular mycorrhizal fungal infection occurred within both the prairie and fen plant species (infection level means ranging from 20% to 47%). Mycorrhizal root infection was significantly correlated with all edaphic factors tested—soil moisture, organic matter, potassium, phosphorus, calcium, magnesium and pH—from May to October 1994. The plant‐mycorrhizal data clearly indicate the presence of mycorrhizae in soils that are saturated or even inundated. The functional role of mycorrhizae in wetlands is still unclear, however. For example, is the species interaction we are observing truly mutualistic or of some other form due to environmental conditions? Arbuscular mycorrhizal fungal relationships in all classes of wetland ecosystems need to be studied further if we are to understand their potential role in the ecological restoration of wetland ecosystems.
Catching Numeric Inconsistencies in Graphs

Numeric inconsistencies are common in real-life knowledge bases and social networks. To catch such errors, we extend graph functional dependencies with linear arithmetic expressions and built-in comparison predicates, referred to as numeric graph dependencies (NGDs). We study fundamental problems for NGDs. We show that their satisfiability, implication, and validation problems are Σp2-complete, Πp2-complete, and coNP-complete, respectively. However, if we allow non-linear arithmetic expressions, even of degree at most 2, the satisfiability and implication problems become undecidable. In other words, NGDs strike a balance between expressivity and complexity. To make practical use of NGDs, we develop an incremental algorithm IncDect to detect errors in a graph G using NGDs in response to updates ΔG to G. We show that the incremental validation problem is coNP-complete. Nonetheless, algorithm IncDect is localizable, i.e., its cost is determined by small neighbors of nodes in ΔG instead of the entire G. Moreover, we parallelize IncDect such that it guarantees to reduce running time with the increase of processors. In addition, to strike a balance between the efficiency and accuracy, we also develop polynomial-time parallel algorithms for detection and incremental detection of top-ranked inconsistencies. Using real-life and synthetic graphs, we experimentally verify the scalability and efficiency of the algorithms.
Subthreshold Region based Linear Feedback Shift Register

Growing demand for portable devices and fast increases in complexity of chip cause power dissipation is an important parameter. Power consumption and dissipation or generations of more heat possess a restriction in the direction of the integration of more transistors. Several methods have been proposed to reduce power dissipation from system level to device level. Subthreshold circuits are widely used in more advanced applications due to ultra low-power consumption. The present work targets on construction of linear feedback shift registers (LFSR) in weak inversion region and their performance observed in terms of parameters like power delay product (PDP). In CMOS circuits subthreshold region of operation allows a low-power for ample utilizations but this advantage get with the penalty of flat speed. For the entrenched and high speed applications, improving the speed of subthreshold designs is essential. To enhance this, operate the devices at maximum current over capacitance. LFSR architectures build with various types of D flip flop and XOR gate circuits are analyzed. Circuit level Simulation is carried out using 130 nm technologies.
Obesity or BMI Paradox? Beneath the Tip of the Iceberg

The obesity paradox refers to extant evidence showing that obesity in older subjects or in patients with several chronic diseases may be protective and associated with decreased mortality. A number of mechanisms have been postulated to support the existence of obesity paradox; however, marked heterogeneity was found across studies and this has cast doubt on the actual presence of this phenomenon. The aim of the present narrative review is to summarize evidence underlying the concept of obesity paradox, focusing on limitations and bias related to this phenomenon, with emphasis on the use of body mass index (BMI). A major cause of the discrepancy between studies may be related to the use of BMI in the definition of obesity, that should consider, instead, excess body fat as the main characteristic of this disease and as the unique determinant of its complications. In addition, the adjustment for potential confounders (e.g., stage and grade of diseases, smoking habit, inability to capture the presence of signs of undernutrition in the normal-weight comparative group, consideration of body composition) may significantly scale down the protective role of obesity in terms of mortality. However, it is still necessary to acknowledge few biases (e.g., reverse causation, attrition bias, selection bias of healthy obese subjects or resilient survivors) that would still apply to obesity even when defined according with body composition. Further research should be prompted in order to promote correct phenotyping of patients in order to capture properly the trajectories of mortality in a number of diseases.
Unity Makes Strength: Exploring Intraspecies and Interspecies Toxin Synergism between Phospholipases A2 and Cytotoxins

Toxin synergism is a complex biochemical phenomenon, where different animal venom proteins interact either directly or indirectly to potentiate toxicity to a level that is above the sum of the toxicities of the individual toxins. This provides the animals possessing venoms with synergistically enhanced toxicity with a metabolic advantage, since less venom is needed to inflict potent toxic effects in prey and predators. Among the toxins that are known for interacting synergistically are cytotoxins from snake venoms, phospholipases A2 from snake and bee venoms, and melittin from bee venom. These toxins may derive a synergistically enhanced toxicity via formation of toxin complexes by hetero-oligomerization. Using a human keratinocyte assay mimicking human epidermis in vitro, we demonstrate and quantify the level of synergistically enhanced toxicity for 12 cytotoxin/melittin-PLA2 combinations using toxins from elapids, vipers, and bees. Moreover, by utilizing an interaction-based assay and by including a wealth of information obtained via a thorough literature review, we speculate and propose a mechanistic model for how toxin synergism in relation to cytotoxicity may be mediated by cytotoxin/melittin and PLA2 complex formation.
Cryopreservation of sperm in Brazilian migratory fish conservation

Simple, effective protocols for cryopreserving milt of five Brazilian migratory characids (Brycon orbignyanus, Prochilodus lineatus, Piaractus mesopotamicus, Salminus maxillosus and Leporinus elongatus) and one Brazilian migratory catfish (Pseudoplatystoma corruscans) are described. Milt was frozen and stored in dry shippers immediately after collection, making the procedure practical for use in the field. A diluent of 5% glucose, 10% dimethyl sulphoxide and 10% egg yolk was effective for all of the characid species, and a diluent of 10% methanol and 15% powdered milk was effective for P. corruscans. Milt was thawed in an ambient temperature water bath (28-30° C). Activation of thawed milt was effective with either saline (0.9 or 0.45% NaCl) or bicarbonate (1% NaHCO 3 ). Fertilization rates with frozen milt varied between 49 and 300% of the control. Application of the technology for increasing genetic diversity in hatchery programmes for enhancement, mitigation or conservation breeding is discussed, as is its application in aquaculture. Inappropriate use of the technology can threaten wild biodiversity and appropriate legislation and education may be required for its responsible use.
Long-term presence and movement patterns of juvenile bull sharks, Carcharhinus leucas, in an estuarine river system

Elasmobranchs living in rivers and estuaries may be highly susceptible to environmental and anthropogenic changes to coastal habitats. To address this, patterns of movement of 67 juvenile bull sharks (Carcharhinus leucas) were examined in the Caloosahatchee River between 2003 and 2006 using an array of 25 acoustic receivers. Individuals were monitored for periods of 1–460 days with most present for periods of weeks to months. Individuals utilised the entire monitored section of the river (∼27 km) and also moved upriver beyond the extent of the acoustic array. Daily activity spaces of individuals ranged from 0 to 14 km with most <5 km. Monthly mean home ranges were 0.9–5.6 km and although home-range sizes were consistent through time, location of individuals within the river changed through time. Individuals moved upstream during the day and downstream at night and this pattern persisted across years. Based on data collected from depth transmitters in 2006, individuals swam closer to the surface at night and remained in deeper water during the day, suggesting further diurnal patterns in habitat use. Long-term consistent use of this habitat by young C. leucas suggests this population is highly dependent on the Caloosahatchee River as a nursery area.
Polar or Charged Residues Located in Four Highly Conserved Motifs Play a Vital Role in the Function or pH Response of a UPF0118 Family Na+(Li+)/H+ Antiporter

Functionally uncharacterized UPF0118 family has been re-designated as autoinducer-2 exporter (AI-2E) family since one of its members, Escherichia coli YdgG, was identified to function as an AI-2E. However, it’s very likely that AI-2E family members may exhibit significantly distinct functions due to low identities between them. Recently, we identified one member of this family designated as UPF0118 to represent a novel class of Na+(Li+)/H+ antiporters. In this study, we presented that UPF0118, together with its homologs, should represent an independent group of AI-2E family, designated as Na+/H+ Antiporter Group. Notably, this group shows five highly conserved motifs designated as Motifs A to E, which are not detected in the majority of AI-2E family members. Functional analysis established that polar or charged residues located in Motif A to D play a vital role in Na+(Li+)/H+ antiport activity or pH response of UPF0118. However, three basic residues located in Motif E are not involved in the function of UPF0118, although the truncation of C terminus resulted in the non-expression of this transporter. Therefore, we propose that E179-R182-K215-Q217-D251-R292-R293-E296-K298-S307 located in Motifs A to D can be used for signature functional motifs to recognize whether AI-2E family members function as Na+(Li+)/H+ antiporters. Current findings positively contribute to the knowledge of molecular mechanism of Na+, Li+ transporting and pH response of UPF0118, and the functional prediction of uncharacterized AI-2E family members.
Entropy Slicing Extraction and Transfer Learning Classification for Early Diagnosis of Alzheimer Diseases with sMRI

Alzheimer’s Disease (AD) is an irreversible neurogenerative disorder that undergoes progressive decline in memory and cognitive function and is characterized by structural brain Magnetic Resonance Images (sMRI). In recent years, sMRI data has played a vital role in the evaluation of brain anatomical changes, leading to early detection of AD through deep networks. The existing AD problems such as preprocessing complexity and unreliability are major concerns at present. To overcome these, a model (FEESCTL) has been proposed with an entropy slicing for feature extraction and Transfer Learning for classification. In the present study, the entropy image slicing method is attempted for selecting the most informative MRI slices during training stages. The ADNI dataset is trained on Transfer Learning adopted by VGG-16 network for classifying the AD with normal individuals. The experimental results reveal that the proposed model has achieved an accuracy level of 93.05%, 86.39%, 92.00% for binary classifications (AD/MCI, MCI/CN, AD/CN) and 93.12% for ternary classification (AD/MCI/CN), respectively, and henceforth the efficiency in diagnosing AD is proved through comparative analysis.
Efeito do genótipo halotano e de diferentes sistemas de produção no desempenho produtivo e na qualidade da carcaça suína

The objective of this study was to evaluate the effect of the halothane genotypes (heterozygous and dominant homozygous) and intensive rearing systems (indoor, wood shavings bedding and outdoor) on growth performance, carcass and meat yield. Ninety six castrated male pigs were used for the trial. Identification of the halothane genotype was determined in blood samples using the DNA-test, based on the polymerase chain reaction (PCR) for amplification of the critical region of the ryanodine receptor and subsequent restriction of the amplified fragment by restriction fragment lengh polymorfism technique (RFLP). Growth and finishing performance were evaluated by weight gain, feed intake and feed efficiency. Carcass quality was evaluated by backfat and muscle depth, meat percentage through Hennessy Grading Probe and carcass weight. Twenty four hours after slaugther, ham and loin weight were recorded and the loin eye area was evaluated. The growth performance was similar for the two genotypes. The heterozygous pigs for the halothane gene had higher percentage of fat-free lean and less fat in the carcass. Outdoor reared pigs showed lower average daily gain and worst efficiency than pigs reared indoor. Carcasses of pigs reared under wood shavings bed had less fat-free lean and greater backfat thickeness. The interaction between halothane genotypes and rearing systems had no significant effect on any trait studied.
Batch-file Operations to Optimize Massive Files Accessing

Existing local file systems, designed to support a typical single-file access mode only, can lead to poor performance when accessing a batch of files, especially small files. This single-file mode essentially serializes accesses to batched files one by one, resulting in a large number of non-sequential, random, and often dependent I/Os between file data and metadata at the storage ends. Such access mode can further worsen the efficiency and performance of applications accessing massive files, such as data migration. We first experimentally analyze the root cause of such inefficiency in batch-file accesses. Then, we propose a novel batch-file access approach, referred to as BFO for its set of optimized Batch-File Operations, by developing novel BFOr and BFOw operations for fundamental read and write processes, respectively, using a two-phase access for metadata and data jointly. The BFO offers dedicated interfaces for batch-file accesses and additional processes integrated into existing file systems without modifying their structures and procedures. In addition, based on BFOr and BFOw, we also propose the novel batch-file migration BFOm to accelerate the data migration for massive small files. We implement a BFO prototype on ext4, one of the most popular file systems. Our evaluation results show that the batch-file read and write performances of BFO are consistently higher than those of the traditional approaches regardless of access patterns, data layouts, and storage media, under synthetic and real-world file sets. BFO improves the read performance by up to 22.4× and 1.8× with HDD and SSD, respectively, and it boosts the write performance by up to 111.4× and 2.9× with HDD and SSD, respectively. BFO also demonstrates consistent performance advantages for data migration in both local and remote situations.
A Discriminative Convolutional Neural Network with Context-aware Attention

Feature representation and feature extraction are two crucial procedures in text mining. Convolutional Neural Networks (CNN) have shown overwhelming success for text-mining tasks, since they are capable of efficiently extracting n-gram features from source data. However, vanilla CNN has its own weaknesses on feature representation and feature extraction. A certain amount of filters in CNN are inevitably duplicate and thus hinder to discriminatively represent a given text. In addition, most existing CNN models extract features in a fixed way (i.e., max pooling) that either limit the CNN to local optimum nor without considering the relation between all features, thereby unable to learn a contextual n-gram features adaptively. In this article, we propose a discriminative CNN with context-aware attention to solve the challenges of vanilla CNN. Specifically, our model mainly encourages discrimination across different filters via maximizing their earth mover distances and estimates the salience of feature candidates by considering the relation between context features. We validate carefully our findings against baselines on five benchmark datasets of classification and two datasets of summarization. The results of the experiments verify the competitive performance of our proposed model.
Bispecific, T-Cell-Recruiting Antibodies in B-Cell Malignancies

Bispecific antibodies (BsAbs) are designed to recognize and bind to two different antigens or epitopes. In the last few decades, BsAbs have been developed within the context of cancer therapies and in particular for the treatment of hematologic B-cell malignancies. To date, more than one hundred different BsAb formats exist, including bispecific T-cell engagers (BiTEs), and new constructs are constantly emerging. Advances in protein engineering have enabled the creation of BsAbs with specific mechanisms of action and clinical applications. Moreover, a better understanding of resistance and evasion mechanisms, as well as advances in the protein engineering and in immunology, will help generating a greater variety of BsAbs to treat various cancer types. This review focuses on T-cell-engaging BsAbs and more precisely on the various BsAb formats currently being studied in the context of B-cell malignancies, on ongoing clinical trials and on the clinical concerns to be taken into account in the development of new BsAbs.
Mesosulfuron-Resistant Italian Ryegrass (Lolium Multiflorum) Biotype from Texas

Acetolactate synthase (ALS)–inhibiting herbicides are often used to control Italian ryegrass in winter wheat in Texas. An Italian ryegrass biotype near Waco, TX was evaluated for resistance to mesosulfuron in field and greenhouse experiments. Control of the biotype in the field was less than 10% with the label rate of mesosulfuron (15 g ai/ha). Greenhouse studies confirmed that the biotype was resistant to mesosulfuron; control of the biotype was less than 35% at 120 g ai/ha mesosulfuron. The herbicide dose required to reduce plant biomass of a susceptible and the Waco biotype by 50% (GR50) was 1.3 and 31 g ai/ha, respectively, indicating a resistance level of 24-fold in the Waco biotype. However, the Waco biotype was controlled with the acetyl-CoA carboxylase inhibitors diclofop and pinoxaden. Nomenclature: Diclofop; mesosulfuron (proposed common name): methyl 2-[[[(4,6-dimethylsulfonyl)amino]methyl]benzoate]; pinoxaden (proposed common name): 8-(2,6-diethyl-4-methylphenyl)-1,2,4,5-tetrahydro-7-oxo-7H-pyrazolo(1,2-d)(1,4,5)oxadiazepin-9-yl 2, 2-dimethylpropanoate; Italian ryegrass, Lolium multiflorum L. LOLMU; wheat, Triticum aestivum L
Novel Role of Endothelial Derived Exosomal HSPA12B in Regulating Macrophage Inflammatory Responses in Polymicrobial Sepsis

Endothelial cell dysfunction contributes to sepsis induced initiate immune response and the infiltration of immune cells into organs, resulting in organ injury. Heat shock protein A12B (HSPA12B) is predominantly expressed in endothelial cells. The present study investigated whether endothelial HSPA12B could regulate macrophage pro-inflammatory response during sepsis. Wild type (WT) and endothelial cell-specific HSPA12B deficient (HSPA12B–/–) mice were subjected to CLP sepsis. Mortality and cardiac function were monitored. Higher mortality, worsened cardiac dysfunction, and greater infiltrated macrophages in the myocardium and spleen were observed in HSPA12B–/– septic mice compared with the WT septic mice. The serum levels of TNF-α and IL-1β were higher and the levels of IL-10 were lower in HSPA12B–/– septic mice than in WT septic mice. Importantly, endothelial exosomes contain HSPA12B which can be uptaken by macrophages. Interestingly, endothelial exosomal HSPA12B significantly increases IL-10 levels and decreases TNF-α and IL-1β production in LPS-stimulated macrophages. Mechanistic studies show that endothelial exosomal HSPA12B downregulates NF-κB activation and nuclear translocation in LPS stimulated macrophages. These data suggest that endothelial HSPA12B plays a novel role in the regulation of macrophage pro-inflammatory response via exosomes during sepsis and that sepsis induced cardiomyopathy and mortality are associated with endothelial cell deficiency of HSPA12B.