Miracle-dz/UniFAR-FTUs huggingface dataset:
An Investigation into Salmonella and Fecal Coliform Contamination of Drinking Water in Broiler Farms in Iran

In view of the effect of water quality on poultry performance, from May to July 2005, the drinking water (source water, pipe water and drinker water) from 40 broiler farms in the rural area of Ahvaz (a city in the southwestern Iran) was sampled to determine the extent of Salmonella & coliform contamination. For Salmonella isolation, 25 ml of water was cultured in 225 ml of lactose broth at 37 C. After 24 hr, the samples o were at first subcultured in TT & SC broths (1:9), and then plated on both BG & SS agars. After purified on blood agar, the suspected colonies were confirmed by usual biochemical & serological tests. Coliform count was carried out as per MPN method. The positive samples were examined for fecal coliform. Coliform counts in 20 farms (50%) were over the max. acceptable level (50 CFU/ml) for poultry water. Fecal coliform was detected in the water of all farms. From the drinker water of 5 farms, Salmonella serotypes Nienstedten, Tinda, Calvinia, Oysterbeds and Sterrenbos were isolated. This is the first report of the isolated serotypes in poultry in Iran.
Nutations in Plant Shoots: Endogenous and Exogenous Factors in the Presence of Mechanical Deformations

We present a three-dimensional morphoelastic rod model capable to describe the morphogenesis of growing plant shoots, as driven by differential growth at the tip. We discuss the evolution laws for endogenous oscillators, straightening mechanisms and reorientations to directional cues, such as phototropic responses to a far light source and gravitropic reactions governed by the statoliths avalanche dynamics. We use this model to investigate the role of elastic deflections due to gravity loading in circumnutating plant shoots. We show that, in the absence of endogenous cues, pendular and circular oscillations arise as a critical length is attained, thus suggesting the occurrence of a Hopf bifurcation reminiscent of flutter instabilities exhibited by structural systems under nonconservative loads. When also oscillations due to endogenous cues are present, their weight relative to those associated with the Hopf instability varies in time as the shoot length and other biomechanical properties change. Thanks to the simultaneous occurrence of these two oscillatory mechanisms, we are able to reproduce a variety of complex behaviors, including trochoid-like patterns, which evolve into circular orbits as the shoot length increases, and the amplitude of the flutter induced oscillations becomes dominant. Our findings suggest that the relative importance of the two mechanisms is an emergent property of the system that is affected by the amplitude of elastic deformations, and highlight the crucial role of elasticity in the analysis of circumnutations.
DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains

Deep neural networks (DNNs) have attained human-level performance on dozens of challenging tasks through an end-to-end deep learning strategy. Deep learning gives rise to data representations with multiple levels of abstraction; however, it does not explicitly provide any insights into the internal operations of DNNs. Its success appeals to neuroscientists not only to apply DNNs to model biological neural systems, but also to adopt concepts and methods from cognitive neuroscience to understand the internal representations of DNNs. Although general deep learning frameworks such as PyTorch and TensorFlow could be used to allow such cross-disciplinary studies, the use of these frameworks typically requires high-level programming expertise and comprehensive mathematical knowledge. A toolbox specifically designed for cognitive neuroscientists to map DNNs and brains is urgently needed. Here, we present DNNBrain, a Python-based toolbox designed for exploring internal representations in both DNNs and the brain. By integrating DNN software packages and well-established brain imaging tools, DNNBrain provides application programming and command line interfaces for a variety of research scenarios, such as extracting DNN activation, probing DNN representations, mapping DNN representations onto the brain, and visualizing DNN representations. We expect that our toolbox will accelerate scientific research in applying DNNs to model biological neural systems and utilizing paradigms of cognitive neuroscience to unveil the black box of DNNs.
Loss of Ubiquitin Ligase STUB1 Amplifies IFNγ-R1/JAK1 Signaling and Sensitizes Tumors to IFNγ

Despite the success of immune checkpoint blockade (ICB) most patients fail to respond durably, in part owing to reduced interferon gamma (IFNγ) sensitivity. Thus, elevating tumor IFNγ-receptor 1 (IFNγ-R1) expression to enhance IFNγ-mediated cytotoxicity is of potential clinical interest. Here, we show that increased IFNγ-R1 expression sensitizes tumors to IFNγ-mediated killing. To unveil the largely undefined mechanism governing IFNγ-R1 expression, we performed a genome-wide CRISPR/Cas9 screen for suppressors of its cell surface abundance. We uncovered STUB1 as key mediator of proteasomal degradation of the IFNγ-R1/JAK1 complex. STUB1 inactivation amplified IFNγ signaling, thereby sensitizing to cytotoxic T cells, but also inducing PD-L1. STUB1 loss in a rational combination with PD-1 blockade strongly inhibited melanomas in vivo. Clinically corroborating these results, a STUB1-KO gene signature was strongly associated with anti-PD-1 response. These results uncover STUB1 as pivotal regulator of IFNγ tumor signaling and provide a rationale for its inhibition combined with anti-PD-1.
Sick Bats Stay Home Alone: Social distancing during the acute phase response in Egyptian fruit bats (Rousettus aegyptiacus)

Along with its many advantages, social roosting imposes a major risk of pathogen transmission. How social animals, and especially free-ranging mammals, reduce this risk is poorly documented. We used lipopolysaccharide injection to imitate bacterial sickness in both a captive and a free-ranging colony of an extremely social, long lived mammal – the Egyptian fruit bat. We monitored behavioral and physiological responses using an arsenal of methods, including on-board GPS and acceleration, video, temperature and weight measurements, and blood samples. Sick-like bats exhibited an increased immune response, as well as classical illness symptoms including fever, weight loss, anorexia, and lethargy. Notably, they also isolated themselves from the group by leaving the social cluster and avoiding contact. Free-ranging individuals ceased foraging outdoors for at least two nights. Together, these sickness behaviors demonstrate a strong, integrative immune response which promotes recovery of infected individuals while protecting their group members from transmission of pathogens, and at the same time, reducing spillover events outside the roost.
Towards a taxonomically unbiased EU Biodiversity Strategy for 2030

Through the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world’s experimental arena for biological conservation. With an estimated budget of €20 billion/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservation trends and status of all protected species. We analyzed LIFE projects focused on animals from 1992 to 2018 and we found that investment towards vertebrates has been six times higher than that for invertebrates (€970 vs €150 million), with birds and mammals alone accounting for 72% species and 75% total budget. Budget allocation is primarily explained by species’ popularity. We propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.
PHYSICAL ACTIVITY AND ABDOMINAL OBESITY STATUS AMONG COMMUNITY AT KG BUKIT BANGKONG, SEPANG, SELANGOR, MALAYSIA

Background: Physically inactivity is known as identifier of a major health impact. Insufficient physical activity is a key risk for non-communicable disease (NCDs) such as cardiovascular diseases, cancer and diabetes. Being physically inactive will also increase the risk of waist abdominal obesity. Therefore, this study has been conducted to determine the prevalence of physical inactivity and abdominal obesity; and its association among community at Kg. Bukit Bangkong, Sepang Selangor.
Acaricidal drug resistance in poultry red mite (Dermanyssus gallinae) and approaches to its management

Poultry red mite (Dermanyssus gallinae), the haematophagous pest of egg laying hens, is an important problem in poultry production in many parts of the world. Control has typically relied on synthetic acaricides in spite of advancements in immunological, biotechnological and genetic approaches. However, the repeated long term use of these compounds has resulted in the development of drug resistant populations of poultry mites, therefore, the availability of effective acaricides is diminishing rapidly. Due to this, there is need for the continuous availability of new chemical acaricides to replace the older types, however the development and registration of new acaricides is a long expensive process, therefore, preserving and maintaining the effectiveness of available acaricides is essential. This review has two parts; the first is to provide the basic understanding of acaricide resistance in D. gallinae while the second part provides more detailed knowledge about the management of resistance to preserve the efficacy of available acaricides.
SOX9 promotes stress-responsive transcription of VGF nerve growth factor inducible gene in kidney epithelial cells

Acute kidney injury (AKI) is a common clinical condition associated with diverse etiologies and abrupt loss of renal function. In patients with sepsis, rhabdomyolysis, cancer, as well as cardiovascular disorders, the underlying disease or associated therapeutic interventions can cause hypoxic, cytotoxic, and inflammatory insults to renal tubular epithelial cells (RTECs) resulting in the onset of AKI. To uncover stress-responsive disease-modifying genes, here we have carried out renal transcriptome profiling in three distinct murine models of AKI. We find that Vgf nerve growth factor inducible gene upregulation is a common transcriptional stress response in RTECs to ischemia, cisplatin, and rhabdomyolysis-associated renal injury. The Vgf gene encodes a secretory peptide precursor protein that has critical neuro-endocrine functions; however, its role in the kidneys remains unknown. Our functional studies show that RTEC-specific Vgf gene ablation exacerbates ischemia, cisplatin, and rhabdomyolysis-associated AKI in vivo and cisplatin-induced RTEC cell death in vitro. Importantly, addback experiments showed that aggravation of cisplatin-induced renal injury caused by Vgf gene ablation is partly reversed by TLQP-21, a Vgf-derived peptide. Finally, in vitro and in vivo mechanistic studies showed that injury-induced Vgf upregulation in RTECs is driven by the transcriptional regulator Sox9. These findings reveal a crucial downstream target of the Sox9-directed transcriptional program and identify Vgf as a stress-responsive protective gene in kidney epithelial cells.
Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.
The role of female search behaviour in determining host plant range in plant feeding insects: a test of the information processing hypothesis

Recent theoretical studies have suggested that host range in herbivorous insects may be more restricted by constraints on information processing on the ovipositing females than by trade–offs in larval feeding efficiency. We have investigated if females from polyphagous species have to pay for their ability to localize and evaluate plants from different species with a lower ability to discriminate between conspecific host plants with differences in quality. Females of the monophagous butterflies Polygonia satyrus, Vanessa indica and Inachis io and the polyphagous P. c–album and Cynthia cardui (all in Lepidoptera, Nymphalidae) were given a simultaneous choice of stinging nettles (Urtica dioica) of different quality. In addition, the same choice trial was given to females from two populations of P. c–album with different degrees of specificity. As predicted from the information processing hypothesis, all specialists discriminated significantly against the bad quality nettle, whereas the generalists laid an equal amount of eggs on both types of nettle. There were no corresponding differences between specialist and generalist larvae in their ability to utilize poor quality leaves. Our study therefore suggests that female host–searching behaviour plays an important role in determining host plant range.
Single-cell analysis of Schistosoma mansoni reveals a conserved genetic program controlling germline stem cell fate

Schistosomes are parasitic flatworms causing one of the most prevalent infectious diseases from which millions of people are currently suffering. Their germline outputs many fertilized eggs, which are both the transmissible agents and the cause of the infection-associated pathology. Given its significance, the schistosome germline has been a research focus for more than a century. Nonetheless, little is known about the molecular mechanisms that regulate its development. Here, we construct a transcriptomic cell type atlas of juvenile schistosomes. This allows us to capture germline stem cells (GSCs) during de novo gonadal development. We identify a genetic program that balances the fate of GSC between proliferation and differentiation. This program is controlled by onecut, a homeobox transcription factor, and boule, an mRNA binding protein. Evaluating this genetic program in schistosome’s free-living evolutionary cousin, the planarian, shows that this germline-specific regulatory program is conserved but its function has changed significantly during evolution.
Topology Proceedings 38 (2011) pp. 237-251: Preserving the Lindel\"{o}f Property Under Forcing Extensions

We investigate preservation of the Lindelöf property of topological spaces under forcing extensions. We give sufficient conditions for a forcing notion to preserve several strengthenings of the Lindelöf property, such as indestructible Lindelöf property, the Rothberger property, and being a Lindelöf P-space.
Hierarchical Linear Disentanglement of Data-Driven Conceptual Spaces

Conceptual spaces are geometric meaning representations in which similar entities are represented by similar vectors. They are widely used in cognitive science, but there has been relatively little work on learning such representations from data. In particular, while standard representation learning methods can be used to induce vector space embeddings from text corpora, these differ from conceptual spaces in two crucial ways. First, the dimensions of a conceptual space correspond to salient semantic features, known as quality dimensions, whereas the dimensions of learned vector space embeddings typically lack any clear interpretation. This has been partially addressed in previous work, which has shown that it is possible to identify directions in learned vector spaces which capture semantic features. Second, conceptual spaces are normally organised into a set of domains, each of which is associated with a separate vector space. In contrast, learned embeddings represent all entities in a single vector space. Our hypothesis in this paper is that such single-space representations are sub-optimal for learning quality dimensions, due to the fact that semantic features are often only relevant to a subset of the entities. We show that this issue can be mitigated by identifying features in a hierarchical fashion. Intuitively, the top-level features split the vector space into different domains, making it possible to subsequently identify domain-specific quality dimensions.
Story Embedding: Learning Distributed Representations of Stories based on Character Networks (Extended Abstract)

This study aims to represent stories in narrative works (i.e., creative works that contain stories) with a fixed-length vector. We apply subgraph-based graph embedding models to dynamic social networks of characters that appeared in stories (character networks). We suppose that interactions between characters reflect the content of stories. We discretize the interactions by discovering the subgraphs and learn representations of stories by predicting occurrences of the subgraphs in corresponding character networks. We find subgraphs rooted in each character on each scene in multiple scales, using the WL (Weisfeiler-Lehman) relabeling process. To predict occurrences of subgraphs, we apply two approaches: (i) considering changes in subgraphs according to scenes and (ii) focusing on subgraphs on the last scene. We evaluated the proposed models by measuring the similarity between real movies with vector representations that were generated by the models.
Population genetics of red spiny lobster (Panulirus interruptus) along the Baja California Peninsula, Mexico

Analysis of the genetic structure of the red spiny lobster (Panulirus interruptus) population was conducted along the Baja California Peninsula, Mexico. Samples for allozyme analysis came from Ensenada, Punta Eugenia, Punta Abreojos, San Juanico, and Bahia Magdalena (about 50 individuals each). Of 16 loci analysed, five were polymorphic (95% criterion) in at least one subpopulation. A significant mean value of FIS = 0.125 indicated some subpopulations departed from Hardy-Weinberg expectations; increased homozygosity was particularly evident for alleles EST-2*b and LAP*a at Ensenada and EST-2*c and EST-4*c at San Juanico. MeanFST = 0.101, which included 99% criterion polymorphic loci, was significant (P < 0.05), supporting a genetic structure throughout the species’ geographical range. Pairwise heterogeneity and FST tests showed no significant differences in allele frequencies between Punta Eugenia and Punta Abreojos, but several pairwise comparisons among the other locations, especially at the most variable loci, showed significant differences, supporting a hypothesis of genetic differentiation of P. interruptus into three subpopulations: southern, central, and northern Baja California. Oceanographic processes, such as semipermanent eddies south of Punta Eugenia that tend to retain phyllosoma larvae, may help generate this pattern. The implications of these findings for the management of the resource are also considered.
Formalizing Group and Propagated Trust in Multi-Agent Systems

We present a formal framework that allows individual and group of agents to reason about their trust toward other agents. In particular, we propose a branching time temporal logic BT which includes operators that express concepts such as everyone trust, distributed trust and propagated trust. We analyze the satisfiability and model checking problems of this logic using a reduction technique.
Predictors of puerperal menstruation

Background Puerperal period is an important and thought-provoking period for puerperal mothers. Surprisingly, reports have indicated that there is increasing number of women resuming menstruation within six weeks of childbirth (puerperal menstruation). To the best of knowledge, there is no prior study on predictors of puerperal menstruation. Objective To determine frequency and predictors of puerperal menstruation. Methods This was a single tertiary health institution cross-sectional study at ESUT Teaching Hospital, Parklane, Enugu, Nigeria that included data from May 2015 to December 2018. Women were interviewed at the end of the first six weeks of their childbirth. Women with HIV positive or had uterine rupture or peripartum hysterectomy were excluded. Bivariate analysis was performed by the chi-squared test and conditional logistic regression analysis was used to determine variables associated with puerperal menstruation. Statistical significance was accepted when P- value is <0.05. Results A total of 371 women met the inclusion criteria. The return of menses within 6 weeks was present in 118(31.8%) women versus 253 (68.2%) women without puerperal menstruation, given a ratio of 1:3. Of the 371 women, 249 (67.1%) were on exclusive breastfeeding. The significant associated risk factors were age (p = 0.009), parity (p<0.001), early use of family planning (p = 0.001), socio-economic status (p<0.001) and manual removal of placenta (p = 0.007). At conditional logistic regression analysis, early use of family planning (p = 0.001), exclusive breastfeeding (p = 0.027) and manual removal of placenta (p = 0.012) were independently associated with puerperal menstruation. Induction/augmentation of labor, postpartum misoprostol use and mode of delivery were not statistically significant (p>0.05, for all) Conclusion One in 3 women resumes menstruation within 6 weeks of childbirth. The major predictor was early initiation of family planning, and exclusive breastfeeding with manual removal of placenta a major protective factor. These interesting issues require further investigation to better understand the mechanism of puerperal menstruation.
Interactive effects of source and recipient habitats on plant invasions: distribution of exotic species in Chile

Most studies on invasibility consider the characteristics of the habitats colonized. However, the success of the establishment of exotic species can be conditioned by the characteristics of the donor communities. In this study, we analyse the extent to which the distribution of exotic herbaceous species in Chile is conditioned either by the climatic characteristics of the recipient area or by the environmental features of the source areas on the Iberian Peninsula.