Miracle-dz/UniFAR-FTUs huggingface dataset:
Dispersal patterns of endogenous bacteria among grass carp (Ctenopharyngodon idellus) guts

The formation and regulation of vertebrate endogenous intestinal microbiota has been widely studied as the microbiota plays a crucial role in the host nutrition, development, and health. Despite the importance of microbiota for host health, it is still unclear whether the endogenous intestinal microorganisms are genetically distinct or whether they are genetically related with each other in different host individuals. In the present study, the dispersal situation of the endogenous intestinal bacteria in grass carp was investigated by constructing bacterial 16S rRNA gene clone libraries. The results indicate that the bacteria harbored in the grass carp gut could be separated into the following two groups: athe private operational taxonomic units (OTUs), which include Cetobacterium somerae, Aeromonas jandaei, Citrobacter freundii, Achromobacter xylosoxidans and Bacteroides species; bthe shared OTUs, which include Vibrio cholerae, Plesiomonas shigelloides and Pasteurella speices. The results obtained in this investigation provide valuable information for assessing the mechanism of spread of the endogenous intestinal bacteria, especially the pathogenic ones. However, the mechanisms involved in different modes of bacterial dispersal in the grass carp gut still require further research.
THE USE OF AGRICULTURAL WASTES AS SUBSTRATES FOR CELL GROWTH AND CARBOXYMETHYL CELLULASE (CMCASE) PRODUCTION BY Bacillus subtilis, Escherichia coli AND Rhizobium sp

Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922 and Rhizobium sp. DASA23010 were examined for carboxymethyl cellulase (CMCase) production. CMCase produced from all strains was characterized as cell-bound enzyme. All strains could grow in medium containing CMC as a sole carbon source. The highest activities obtained from B. subtilis, E. coli and Rhizobium sp. were not significantly different. Comparing the growth in three agricultural wastes, maximum cell numbers were obtained from the media containing pineapple peel, vegetable residue and corncob, respectively. Corncob stimulated higher production of CMCase than other agricultural wastes.
Abstract. Delayed neurological deterioration in the absence of direct cord insult following surgical removal and cord decompression is a rare but severe postoperative complication in a small subset of patients with intraspinal meningiomas

Delayed neurological deterioration in the absence of direct cord insult following surgical removal and cord decompression is a rare but severe postoperative complication in a small subset of patients with intraspinal meningiomas. To date, the underlying pathophysiology of such a finding remains unclear and ischemia-reperfusion injury (IRI) is considered as the potential etiology in the literature. However, no experimental research has been reported to prove this hypothesis. The present study investigated whether IRI occurs following decompression surgery using an experimental rat model of chronic compressive spinal cord injury (SCI). A chronic spinal cord compression model was developed with various sizes of polymer sheets (mild and severe compression) that were microsurgically implanted underneath the T8-9 laminae, and occurrence of IRI in the spinal cord following decompression was determined by measuring superoxide dismutase (SOD) level and malondialdehyde (MDA) concentration. In the mild compression groups, after decompression SOD activities significantly increased along with a reduction in MDA content compared with the non-decompression group (P<0.05), which exhibited diminishment of lipid peroxidation and relief of the secondary injury. These findings indicated that decompression is effective to improve neurological recovery and may deliver improved outcomes for chronic mild compression of the spinal cord. However, in severe compression groups, after decompression, SOD activities markedly reduced further along with a significant increase in MDA content compared with non-decompression group (P<0.05). The results indicated that lipid peroxidation increased immediately after decompression surgery which resulted from reperfusion of the spinal cord. These findings demonstrated IRI may occur as a result of chronic severe compression of the spinal cord. In clinical practice, sudden cord expansion and reperfusion may have lead to disruption in the blood spinal cord barrier, and triggered a cascade of IRI resulting in postoperative neurologic deterioration. Recognition of this neurological deterioration following removal for intraspinal meningiomas may improve preoperative patient counseling and merits further study for determination of the precise pathophysiology.
Comparison of formaldehyde exposure measurements stored in French and German databases

Workplace formaldehyde measurements stored in the German MEGA database and the French COLCHIC database were studied. Industrial sectors in which formaldehyde is most often sampled were used to provide results in both countries. The results show that formaldehyde is often found in human health activities and in the manufacture of wood products, basic metals, rubber and plastic products, and textiles. MEGA and COLCHIC data for these sectors are presented by type of measurement (area and personal sampling). The results also show formaldehyde exposures in the major industrial sectors in both countries. The exposure data stored in MEGA and COLCHIC present similar magnitude. A broad picture of occupational exposure to formaldehyde in France and Germany was obtained by comparing the data from the
Speech Recognition for Accented English

In recent years, deep neural networks have become the state of the art for speech recognition. However, speech recognition systems (both neural and Hidden Markov Model based) often struggle to correctly interpret foreign accents (1). We aim to contribute to the body of literature on fairness in machine learning by demonstrating that it is possible to improve the performance of deep neural networks on accented English speech by adding an adversary to the training architecture. This adversary adjusts the loss function of the speech recognition network in a way that enforces parity in the loss attributed to speech examples from American and non-American English speakers. Although our results are not statistically signiﬁcant, we found that adding an adversary to the model architecture did decrease the gap in both WER and CER for the two accent classes. We hypothesize that training a larger model that achieves better results on the test set would yield more convincing results that adversarial architectures are useful for enforcing fairness in NLP applications.
Music Recommendation for Podcast Scripts: Detecting Emotion from Text

In this project, our task is to generate music recommendations based on podcast scripts. Given a podcast script, our model will detect the emotion from the text to recommend relevant music. To achieve this, our model has been trained on a Twitter dataset with labelled emotions. Then, the model will be trained on podcast scripts through domain adaptation. Initial approaches include building a CNN, LSTM, RNN, BERT
Effect of feeding various dosages of Saccharomyces cerevisiae fermentation product on health, reproduction, and costs in multiparous dairy cows

Increased nutritional demands and suppressed immune function increase the risk for metabolic and infectious diseases in dairy cows during the transition period. These problems increase with parity number and result in significant losses in milk production and early culling. Supplementation of Saccharomyces cerevisiae fermentation product (Diamond V Original XPTM; XP) may support immune function and greater nutritional demands; hence, XP may decrease the risk of infectious and metabolic diseases. Doubling feeding rates of XP may provide greater health benefits to dairy cows. The objective of the current study was to evaluate whether feeding a single or double dose of XP during the transition period (-4 to 4 wks postpartum) may decrease the risk of metabolic and infectious diseases in multiparous dairy cows. Multiparous Holstein cows, housed in the same pen, were given a supplement containing 0 (n = 54), 56 (n = 52), or 112 g (n = 54) of XP daily during morning lock-up as a top dressing to their TMR. The supplement consisted of 0, 56, or 112 g of XP mixed with 84 g of molasses and 168, 112, or 56 g of corn meal, respectively. Intake of the supplement was monitored. The incidence and treatment period of ketosis, retained placenta, metritis, mastitis, udder edema, and was recorded for each cows in the first 100 d postpartum. Somatic cell score was analyzed from DHIA records taken twice weekly on non-consecutive days for the first 4 wks postpartum. Feeding XP improved supplement intake at parturition (P = 0.02) and decreased the incidence and treatment length of clinical mastitis (P = 0.02 and P = 0.08) and somatic cell scores in milk (P = 0.08). Feeding a double dose of XP additionally tended to decrease the incidence and duration of udder edema (P = 0.09 and P = 0.07) and days lost due to early culling or death (P = 0.05). We conclude that supplementation of Saccharomyces cerevisiae fermentation product (XP) may support mammary health and act as an appetite
Exploring T EXT F OOLER ’s Syntactically-and Semantically-Sound Distributed Adversarial Attack Methodology

T EXT F OOLER [1] is a recent adversarial attack model that establishes itself to be a potentially devastating method against a diverse set of NLP models, including the well-acclaimed BERT[2] model. However, much of T EXT F OOLER ’s methodology is chosen simply based upon intuition and lacks direct comparison to alternative substitutions within its attack pipeline. This project explores the performance of the vanilla T EXT F OOLER model compared to standard variations commonly seen in other adversarial attack methods, and validates the methodology proposed by the original authors. Conducted experiments substituted white-box, distributional sampling, and transformer-based semantic similarity metrics in place of their equivalent counterparts in T EXT F OOLER ’s original methodology. However, within the context of binary classiﬁcation, empirical results suggest the original T EXT F OOLER method to be most robust and effective against multiple types of sequence classiﬁcation, despite failing to sufﬁciently meet human evaluations of semantic similarity.
Question Answering on Adversarial SQuAD 2.0

Many seemingly successful question answering (QA) systems fail against simple adversarial inputs, such as syntactically similar sentences about different topics, demonstrating a lack of true language understanding. Investigating what makes QA systems more successful against adversarial input can help make NLP systems more successful overall. We implement an iterative output layer for a BiDAF-based model and a QANet-based model, achieving modest gains on both non-adversarial and adversarial datasets with the former. We also describe a method to extend existing adversarial datasets generated based on SQuAD 1.1, to become more representative of SQuAD 2.0.
Etude du rôle des homologues de DC-SIGN dans le modèle murin d'infection par Mycobacterium tuberculosis

Tuberculosis (TB) is due to the infection by Mycobacterium tuberculosis (M. Tb). The interaction between the bacilli and the pathogen recognition receptors regulate the innate immune response to the pathogen but can also contribute to the development of the pathology. DC-SIGN is a C-type lectin which interacts with M. Tb may play an important role in human TB, which remained to be further investigated. To better understand the role of DC-SIGN in anti-mycobacterial immunity, we have used the murine model of M. Tb infection. Among the eight murine homologues (SIGNR1 to 8), SIGNR1 and SIGNR3 are the most similar homologues to DC-SIGN The infection of the mouse lines inactivated in those 2 candidates and SIGNR5 have shown that only SIGNR3-deficient mice display a higher susceptibility to the early phases of infection. Like DC-SIGN, SIGNR3 is induced in pulmonary phagocytes in infected animals. SIGNR3 can recognize glycosylated mycobacterial ligands and the whole bacteria to allow their internalization and to induce the secretion of effectors of the immune response. In vitro, we have shown that SIGNR3 signaling is dependent on a tyrosine motif and relies on the kinase SYK which activates the immune-modulatory transduction cascade. Our results suggest that SIGNR3 is the functional homologue of DC-SIGN and contributes to the protection of the host. Preliminary results suggest that DC-SIGN stimulation may also promote the secretion of pro-inflammatory cytokines in human macrophages. In summary, our results challenge the current dogma on the role of DC-SIGN as an immune escape receptor, and rather suggest that DC-SIGN may be a key-component of the defense system against M. Tb and possibly other pathogens, which remains to be evaluated in human.
Succession of wood-inhabiting fungal communities

Dead wood constitutes an important substrate for biodiversity in boreal forests. As the wood decays, fungal communities develop and species associations are formed. Species interactions are thought to affect community development, but the mycelial dynamics within fungal communities are poorly understood. In this thesis the diversity and temporal dynamics within fungal communities in Norway spruce logs are studied. In particular, patterns of diversity and mechanisms during community assembly are investigated. 454 sequencing is applied to study the less well-known fungal diversity and fine-scale mycelial distribution patterns in decaying logs. The influence of priority effects during community assembly is studied using time-series data from re-inventoried logs. The importance of wood-modification by a primary species and competition is examined in species interaction laboratory experiments. 454 sequencing revealed species-rich fungal communities with diverse ecological roles. Wood-decaying basidiomycetes was found to be the most abundant ecological group, and saprotrophic, mycorrhizal and parasitic fungi were regularly detected. Mycobiont partners of lichens were isolated from interior parts of logs. Fine-scale distribution within logs revealed that resource utilization reflects the life histories of fungal taxa. More decayed samples hosted a higher number of taxa, particularly ascomycetes, whereas wood-decaying basidiomycetes were found in less decayed wood. Priority effects in terms of different mortality factors of trees and the presence of primary decay species were found to affect the subsequent community composition. A species-specific response to primary decay and antagonistic interactions significantly affected decay rate and growth. It is concluded that priority effects are more important in early stages of community development while species more frequent in middle stages of decomposition relies more upon competitive abilities.
Approximating two value functions instead of one: towards characterizing a new family of Deep Reinforcement Learning algorithms

This paper makes one step forward towards characterizing a new family of model-free Deep Reinforcement Learning (DRL) algorithms. The aim of these algorithms is to jointly learn an approximation of the state-value function ( V ), alongside an approximation of the state-action value function ( Q ). Our analysis starts with a thorough study of the Deep Quality-Value Learning (DQV) algorithm, a DRL algorithm which has been shown to outperform popular techniques such as Deep-Q-Learning (DQN) and Double-Deep-Q-Learning (DDQN) [16]. Intending to investigate why DQV’s learning dynamics allow this algorithm to perform so well, we formulate a set of research questions which help us characterize a new family of DRL algorithms. Among our results, we present some speciﬁc cases in which DQV’s performance can get harmed and introduce a novel off-policy DRL algorithm, called DQV-Max, which can outperform DQV. We then study the behavior of the V and Q functions that are learned by DQV and DQV-Max and show that both algorithms might perform so well on several DRL test-beds because they are less prone to suffer from the overestimation bias of the Q function.
Using Probabilistic Context-Free Grammars

In this paper, we present a novel approach for authorship attribution, the task of identifying the author of a document, using probabilistic context-free grammars. Our approach involves building a probabilistic context-free grammar for each author and using this grammar as a language model for classification. We evaluate the performance of our method on a wide range of datasets to demonstrate its efficacy.
A Close Examination of Factual Correctness Evaluation in Abstractive Summarization

Generating fabricated facts has been a long-standing problem of abstractive summarization models, and has signiﬁcantly limited their applicability in practice. Previous works about improving factual correctness only rely on human evaluations, which weakens the transparency and reproducibility. In this work, we aim to examine how to evaluate factual correctness. We start with a human study to thoroughly understand what affects factual correctness evaluations
PTEM: A popularity-based topical expertise model for community question answering

Community Question Answering (CQA) websites are widely used in sharing knowledge, where users can ask questions, reply answers, and evaluate answers. So far, the evaluation of answers has been explained by the contents of answers through the investigation of users’ topics of interest and expertise levels. In this paper, we focus on modeling the user’s evaluation behavior in that users can see the an-swerer’s proﬁle as well as the answer content before evaluating the quality of the answer. We propose a model called Popularity-based Topical Expertise Model (PTEM), a generative model to analyze the rich-get-richer phenomenon that popular user’s answers are more recommended. We can simultaneously estimate the topical expertise of each user and the strength of the rich-get-richer eﬀect through the EM algorithm combined with collapsed Gibbs sampling. Experiments are performed on the StackExchange data, and the results demonstrate a rich-get-richer phenomenon in the community. We further discuss the superiority and usefulness of the proposed model through analysis in the discipline of philosophy.
The Inflammatory Biomarkers as Predictors of Decreased Number of Mononuclear Progenitor Cells in Patients with Metabolic Syndrome and Type 2 Diabetes Mellitus

Introduction: Metabolic disorders remain a leading contributor to cardiovascular mortality worldwide. Circulating endothelial progenitor cells (EPCs) are decreased in metabolic disorders, thus identifying the different populations of EPCs could assist in prognosis. This study was conducted to investigate the population of circulating endothelial progenitor cells (EPCs) in patients with type two diabetes mellitus (T2DM) or metabolic syndrome (MetS). Materials and Methods: The study retrospectively involved 101 patients (54 subjects with T2DM and 47 patients with MetS) and 35 healthy volunteers. Flow cytometry was used for detecting EPCs using CD45, CD34, CD14, Tie-2, and VEGFR2 (CD309) markers, which were measured at the beginning of the study. Results: There is a significant difference between the median total number and frequency of CD14/ CD309+ and CD14/CD309/Tie2+ in patients with dysmetabolic disorders vs control. CD14/CD309+ and CD14/CD309/Tie2+ EPCs were 19% and 14% higher among MetS subjects in comparison with T2DM patients. Osteoprotegerin (OPG) and hs-C-reactive protein (hs-CRP), significantly improved the predictive model based on T2DM + number of multiple cardiovascular risk factors (MCRFs)>3 for both subsets of EPCs. Among patient study population for category-free NRI, 5% of events and 11% of nonevents were correctly reclassified by the addition of hs-CRP and OPG to the base model for decreased absolute number of circulating EPCs labeled CD14+CD309+. Therefore, 6% of events and 14% of nonevents were correctly reclassified using category-free NRI for depleted CD14+CD309+Tie2+ EPCs Conclusions: In conclusion, we suggest that inflammatory biomarkers (hs-CRP, OPG) could be a predictor for decreased CD14+CD309+ and CD14+CD309+Tie2+ EPCs among dysmetabolic patients, without preexisting atherosclerotic lesions of coronary arteries. The Inflammatory Biomarkers as Predictors of Decreased Number of Mononuclear Progenitor Cells in Patients with Metabolic Syndrome and Type 2 Diabetes Mellitus Publication History: Received: March 03, 2017 Accepted: July 25, 2017 Published: July 27, 2017
Service Network Design for Same-Day Delivery with Hub Capacity Constraints

We study a new service network design problem for an urban same-day delivery system in which the number of vehicles that can simultaneously load or unload at a hub is limited. Due to the presence of both time constraints for the commodities and capacity constraints at the hubs, it is no longer guaranteed that a feasible solution exists. The problem can be modeled on a time-expanded network and formulated as an integer program. To be able to solve real-world instances, we design and implement three heuristics: (1) an integer programming–based heuristic, (2) a metaheuristic, and (3) a hybrid matheuristic. An extensive computational study using real-world instances (with different geographies, market sizes, and service offerings) from one of China’s leading comprehensive express logistics service providers demonstrates the efficacy of the three heuristics.
Resuspension of Sediments by Watercraft Operated in Shallow Water Habitats of Anne Arundel County, Maryland

Shallow water habitats rank among the most important components of the Chesapeake Bay ecosystem. The operation of watercraft in these sensitive environments increases the hydrodynamic energy of the site through the generation of surface wakes and propeller wash. When this energy exceeds the shear force of sediment material, sediment resuspension occurs. The degree and pattern of resuspension determine the impact to resident biota. In this study, a variety of common recreational watercraft were operated in the navigable headwaters of seven creeks in the mid-Chesapeake Bay area. The craft were operated according to existing regulations and the rules of good seamanship along an established course that ranged in depth from 0.3 to 1.8 m. Bottom sediments from the courses on each creek were analyzed for texture prior to testing. During testing, turbidity was measured in Nephelometer Turbidity Units (NTU) at the surface, middle, and bottom of the water column at each of the depths. No significant differences in turbidity were found among the 10 watercraft (ranging from a personal watercraft to a 235 hp displacement hull vessel) tested on the different creeks; however, when resuspension was intentionally induced, only turbidity at the lower portions of the water column was significantly increased. This suggests that studies of this type require sampling throughout the water column in order to fully evaluate potential adverse effects on sediment stability, regardless of the source. INDEX WORDS: Sediment resuspension, turbidity, boat wake. INTRODUCTION Shallow water habitats have been identified as one of the most important components of the Chesapeake Bay ecosystem. These areas, which are mostly located along the shorelines of the bay and its tributaries, are the habitat of rich and diverse plant communities. These communities, which include freshwater nontidal wetlands, tidal emergent wetlands and submergent wetlands, have been shown to be essential for maintaining water quality and biological productivity of aquatic ecosystems. Wetlands stabilize sediments, participate in aquatic nutrient