Miracle-dz/UniFAR-FTUs huggingface dataset:
Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety

The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.
Locating Organizations and Their Methods in Registrations of Clinical Migraine Trials: Analysis of ClinicalTrials.gov

Background and Objective: ClinicalTrials.gov is a centralized venue for monitoring clinical research and allows access to information on publicly and privately funded studies. To better recognize influential institutions in the field of headache, we identified major organizations conducting clinical trials in migraine research. Furthermore, we examined the frequency of different study designs. Methods: Utilizing the ClinicalTrials.gov application programming interface, we extracted studies including individuals with migraine from February 29, 2000, to July 28, 2020, for the following: (1) host organization, (2) study type, (3) primary purpose, (4) intervention model, and (5) allocation. Results: We included 921 entries encompassing 423 organizations. Thirty-two organizations produced ≥5 entries each and 40.0% of all entries. Most, 86%, were interventional studies while 13.6% were observational studies. The most common study design had a randomized allocation of participants. The most frequent primary purpose was treatment (62.4%) followed by prevention (13.0%). There were 56.9% parallel assignment models, 15.2% single group assignment models, and 12.4% crossover assignment models. Conclusion: A minority of organizations contribute to a significant number of registrations of clinical migraine trials, suggesting that clinical research in migraine is oligarchic. The most common study is interventional and randomized, with parallel assignment of participants with treatment as the primary purpose. This likely reflects the need to evaluate novel putative pharmacological medications.
Pancreatic Cancer Progression Is Regulated by IPO7/p53/LncRNA MALAT1/MiR-129-5p Positive Feedback Loop

Background: Pancreatic cancer is a malignancy with poor prognosis. Importin 7 (IPO7) is a soluble nuclear transport factor, which has been linked to the pathogenesis of several human diseases. However, its role and underlying mechanism in pancreatic cancer are still obscure. Methods: Immunohistochemical staining and quantitative real-time polymerase chain reaction (qPCR) were performed to determine IPO7 expression in pancreatic cancer tissues and adjacent tissues. Western blot was used to measure IPO7 expression at the protein level in cell lines. Cell Counting Kit-8 (CCK-8), 5-bromo-2′-deoxyuridine (BrdU), flow cytometry, and Transwell assays were employed to explore the biological functions of IPO7. Subcutaneous xenograft transplanted tumor model and caudal vein injection model in mice were also established to validate the oncogenic role of IPO7. Western blot and qPCR were utilized to detect the regulatory function of IPO7 on p53 and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), respectively. Interaction between MALAT1 and miR-129-5p and interaction between miR-129-5p and IPO7 were verified by bioinformatics prediction, qPCR, dual-luciferase reporter gene experiment, RNA immunoprecipitation (RIP), and pull-down assay. Results: Upregulation of IPO7 in pancreatic cancer tissues was associated with adverse prognosis of the patients with pancreatic cancer. Knocking down IPO7 remarkably suppressed cancer cell proliferation and metastasis, while it promoted apoptosis. Overexpression of IPO7 facilitated the malignant phenotypes of pancreatic cancer cells. Mechanistically, IPO7 could repress the expression of p53 and induce the expression of MALAT1 but reduce miR-129-5p expression. Furthermore, miR-129-5p was identified as a posttranscriptional regulator for IPO7, and its inhibition led to IPO7 overexpression in pancreatic cancer cells. Conclusion: IPO7 is a novel oncogene for pancreatic cancer, and IPO7/p53/MALAT1/miR-129-5p positive feedback loop facilitates the progression of this deadly disease. Graphical Abstract IPO7 is a novel oncogene for pancreatic cancer, and IPO7/p53/MALAT1/miR-129-5p positive feedback loop facilitates the progression of this deadly disease.
Semen-Derived Exosomes Mediate Immune Escape and Transmission of Reticuloendotheliosis Virus

Reticuloendotheliosis virus (REV) causes immune-suppression disease in poultry, leading to a significant economic burden worldwide. Recent evidence demonstrated that the REV can enter the semen and then induce artificial insemination, but how the virus gets into semen was little known. Accumulating studies indicated that exosomes serve as vehicles for virus transmission, but the role of exosomes in viral shedding through the semen remains unclear. In this study, exosomes purified from the REV-positive semen were shown with reverse transcription-PCR and mass spectrometry to contain viral genomic RNA and viral proteins, which could also establish productive infections both in vivo and in vitro and escape from the REV-specific neutralizing antibodies. More importantly, compared with the infection caused by free virions, the exosome is more efficient for the virus to ensure effective infection and replication, which can also help the REV compromise the efficacy of the host immune response. In summary, this study demonstrated that semen-derived exosomes can medicate the transmission and immune escape of REV, implicating a novel mechanism for REV entering the semen and leading to vertical transmission.
The “Sweet Spot” in the Middle: Why Do Mid-Scale Farms Adopt Diversification Practices at Higher Rates?

In the past few decades, farmers and researchers have firmly established that biologically diversified farming systems improve ecosystem services both on and off the farm, producing economic benefits for farmers and ecological benefits for surrounding landscapes. However, adoption of these practices has been slow, requiring a more nuanced examination of both barriers and opportunities to improve adoption rates. While previous research has demonstrated that both individual and structural factors shape farmers' decisions about whether to adopt diversification practices, this study aims to understand the interaction of these individual and structural factors, and how they relate to farm scale. Based on 20 interviews with organic lettuce growers on the Central Coast of California, as well as 8 interviews with technical assistance providers who work with these growers, we constructed a typology to help elucidate the distinct contexts that shape growers' decisions about diversification practices. This typology, which reflects the structural influence of land rent and supply chains, divides growers into three categories: limited resource, mid-scale diversified, or wholesale. In this economic context, limited resource and wholesale growers both experience significant barriers that constrain the adoption of diversification practices, while some mid-scale diversified growers have found a “sweet spot” for managing agroecosystems that can succeed in both economic and ecological terms. The key enabling factors that allow these farmers to choose diversification, however, are not directly related to their farm size, but have more to do with secure land tenure, adequate access to capital and resources, and buyers who share their values and are willing to pay a premium. By focusing on these key enabling factors with targeted policies, we believe it is possible to encourage diversification practices on farms at a variety of scales within California's Central Coast.
Integrated Analysis of the Transcriptome and Metabolome Reveals Genes Involved in Terpenoid and Flavonoid Biosynthesis in the Loblolly Pine (Pinus taeda L.)

Loblolly pine (Pinus taeda L.) is an important tree for afforestation with substantial economic and ecological value. Many metabolites with pharmacological activities are present in the tissues of P. taeda. However, the biosynthesis regulatory mechanisms of these metabolites are poorly understood. In the present study, transcriptome and metabolome analyses were performed on five tissues of P. taeda. A total of 40.4 million clean reads were obtained and assembled into 108,663 unigenes. These were compared with five databases, revealing 39,576 annotated unigenes. A total of 13,491 differentially expressed genes (DEGs) were observed in 10 comparison groups. Of these, 487 unigenes exhibited significantly different expressions in specific tissues of P. taeda. The DEGs were explored using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis. We identified 343 and 173 candidate unigenes related to the biosynthesis of terpenoids and flavonoids, respectively. These included 62 R2R3-MYB, 30 MYB, 15 WRKY, seven bHLH, seven ERF, six ZIP, five AP2, and one WD40 genes that acted as regulators in flavonoid and/or terpenoid biosynthesis. Additionally, metabolomics analysis detected 528 metabolites, among which 168 were flavonoids. A total of 493 differentially accumulated metabolites (DAMs) were obtained in 10 comparison groups. The 3,7-Di-O-methyl quercetin was differentially accumulated in all the comparison groups. The combined transcriptome and metabolome analyses revealed 219 DEGs that were significantly correlated with 45 DAMs. Our study provides valuable genomic and metabolome information for understanding P. taeda at the molecular level, providing a foundation for the further development of P. taeda-related pharmaceutical industry.
Modest de novo Reactivation of Single HIV-1 Proviruses in Peripheral CD4+ T Cells by Romidepsin

A cure for human immunodeficiency virus (HIV-1) is restricted by the continued presence of a latent reservoir of memory CD4+ T cells with proviruses integrated into their DNA despite suppressive antiretroviral therapy (ART). A predominant strategy currently pursued in HIV-1 cure-related research is the “kick and kill” approach, where latency reversal agents (LRAs) are used to reactivate transcription from integrated proviruses. The premise of this approach is that “kicking” latent virus out of hiding allows the host immune system to recognize and kill infected cells. Clinical trials investigating the efficacy of LRAs, such as romidepsin, have shown that these interventions do induce transient spikes in viral RNA in HIV-1-infected individuals. However, since these trials failed to significantly reduce viral reservoir size or significantly delay time to viral rebound during analytical treatment interruptions, it is questioned how much each individual latent provirus is actually “kicked” to produce viral transcripts and/or proteins by the LRA. Here, we developed sensitive and specific digital droplet PCR-based assays with single-provirus level resolution. Combining these assays allowed us to interrogate the level of viral RNA transcripts from single proviruses in individuals on suppressive ART with or without concomitant romidepsin treatment. Small numbers of proviruses in peripheral blood memory CD4+ T cells were triggered to become marginally transcriptionally active upon romidepsin treatment. These novel assays can be applied retrospectively and prospectively in HIV-1 cure-related clinical trials to gain crucial insights into LRA efficacy at the single provirus level.
Understanding Variable Motor Responses to Direct Electrical Stimulation of the Human Motor Cortex During Brain Surgery

Direct electrical stimulation of the brain is the gold standard technique used to define functional-anatomical relationships during neurosurgical procedures. Areas that respond to stimulation are considered “critical nodes” of circuits that must remain intact for the subject to maintain the ability to perform certain functions, like moving and speaking. Despite its routine use, the neurophysiology underlying downstream motor responses to electrical stimulation of the brain, such as muscle contraction or movement arrest, is poorly understood. Furthermore, varying and sometimes counterintuitive responses can be seen depending on how and where the stimulation is applied, even within the human primary motor cortex. Therefore, here we review relevant neuroanatomy of the human motor system, provide a brief historical perspective on electrical brain stimulation, explore mechanistic variations in stimulation applications, examine neurophysiological properties of different parts of the motor system, and suggest areas of future research that can promote a better understanding of the interaction between electrical stimulation of the brain and its function.
Immunomodulatory Effects of Tryptophan Metabolism in the Glioma Tumor Microenvironment

Gliomas are the most common primary malignant tumor in adults’ central nervous system. While current research on glioma treatment is advancing rapidly, there is still no breakthrough in long-term treatment. Abnormalities in the immune regulatory mechanism in the tumor microenvironment are essential to tumor cell survival. The alteration of amino acid metabolism is considered a sign of tumor cells, significantly impacting tumor cells and immune regulation mechanisms in the tumor microenvironment. Despite the fact that the metabolism of tryptophan in tumors is currently discussed in the literature, we herein focused on reviewing the immune regulation of tryptophan metabolism in the tumor microenvironment of gliomas and analyzed possible immune targets. The objective is to identify potential targets for the treatment of glioma and improve the efficiency of immunotherapy.
Reviews Are Gold!? On the Link between Item Reviews and Item Preferences (Long paper)

User-user similarities in recommender systems are traditionally assessed on co-rated items. As ratings encode item preferences,similaritiesonco-rateditemscapturesimilaritiesinitempreferences. However,amajorityofsimilaritiesareundefined as particularly small profiles seldom overlap. We propose to use a similarity measure based on users’ item reviews in order to estimate similarities in item preferences in the absence of co-rated items. Although it is commonly believed that item reviews are descriptive of a user’s item preferences, it is not clear whether indeed and what about a user’s item preferences item reviews describe. We present empirical results indicating that the proposed review-based similarity measure captures features in users’ item preferences that are different from those captured on co-rated items. Astonishingly, we find that 10 keywords of a user’s item reviews suffice to represent a user’s item preferences. Independently, we argue that the proposed review-based similarity measure is particularly suitable for use in decentralized recommender systems for three design properties. First, it can be calculated between any pair of users who hold item reviews. Second, it can be calculated bilaterally without involvement of a third party. And third, it does not require to reveal a user’s plain review text.
A Test Suite for JSON Schema Containment

JSON is a very popular data exchange format, and JSON Schema an increasingly popular schema language for JSON. Evidently, schemas play an important role in implementing conceptual models. For JSON Schema, there is a ﬁrst generation of tools for checking whether one schema is contained in another. This is an important task when comparing schemas, and ultimately, the conceptual models that they capture. Testing whether such tool implementations are correct is diﬃ-cult, since writing test cases requires a deep understanding of the JSON Schema language. In this demo, we present the ﬁrst systematically generated test suite for JSON Schema containment checking. This test suite consists of pairs of schemas where the containment relationship is known by construction . Our test suite aims at covering all language features of JSON Schema. Applying existing containment checkers (including our own implementation) to our test suite, we discovered implementation bugs not known to us. We oﬀer our test suite to the research community as well as to tool developers, hoping to contribute to the development of JSON Schema containment checkers.
Case Study on the Development of a Recommender for Apple Disease Diagnosis with a Knowledge-based Bayesian Network (Long paper)

This paper presents a case-study of a knowledge-based recommender system capable to diagnose post-harvest diseases of apples. It describes the process of knowledge elicitation and construction of a Bayesian Network reasoning system as well as its evaluation with three different types of studies involving diseased apples. The ground truth of diseased instances has been established by genome sequencing in a lab. The paper demonstrates the performance differences of knowledge-based reasoning mechanisms due to different users interacting with the system under different conditions and proposes methods for boosting the performance by likelihood evidence learned from the estimated consensus of users’ and expert’s interactions.
The Sentence End and Punctuation Prediction in NLG Text (SEPP-NLG) Shared Task 2021

This paper describes the ﬁrst Sentence End and Punctuation Prediction in Natural Language Generation (SEPP-NLG) shared task 1 held at the SwissText conference 2021. The goal of the shared task was to develop solutions for the identiﬁcation of sentence boundaries and the insertion of punctuation marks into texts produced by NLG systems. The data and submissions 2 , and the codebase 3 for the shared tasks are publicly available.
A flyweight and superelastic graphene aerogel as a high-capacity adsorbent and highly sensitive pressure sensor

The preparation of ultralight, superelastic and multifunctional graphene aerogels still remains a challenge. Herein we develop a silane-crosslinked and modified graphene aerogel (SGA) using a novel and simple method of chemical vapor deposition of methyltriethoxysilane into graphene oxide aerogels. The SGA is mechanically robust and shows fantastic properties satisfying multiple applications. Firstly, the SGA exhibits hitherto the highest compression recoverability (99.5%), as well as a high energy loss coefficient and cycle stability. Secondly, the compressible and ultralight (minimum density of 0.35 mg cm−3) SGA could serve as a fast and recyclable superadsorbent being able to adsorb various organic liquids with ultrahigh capacity (>1000 g g−1), which is almost the highest value among known adsorbents. Moreover, the electrical resistance of SGA is highly sensitive to compressive strain and applied pressure due to the enhanced connection between adjacent graphene sheets, which makes the SGA a great pressure sensor with high sensitivity (−67.1 kPa−1) and a low detection limit (<30 Pa); the SGA demonstrates great potential in real-time monitoring of subtle actions like the beat of water droplets. Therefore, the flyweight and mechanically robust SGA holds fantastic properties and great potential in multiple applications.
Calcium-Doped Y114 Layered Cobalt Perovskite, a Promising Anodic Material for Direct Methanol Fuel Cell

In this paper, calcium doped cobalt layered perovskite type 114 electrode electrocatalytic activity for methanol oxidation reaction (MOR) in aqueous alkaline solution (1 M KOH) has been investigated in order to find the relationship between methanol concentration in the solution and oxidation potential, current density, and oxidation efficiency. For a complete characterization of MOR on this electrode, several electrochemical methods were used: chronoamperometry, chronopotentiometry, chronocoulometry. Also, in order to understand the oxidation mechanism, kinetic parameters were determined using Tafel method and electrochemical impedance spectroscopy (EIS) was performed. MOR on layered cobalt perovskite electrodes becomes a serious issue, especially due to their use as anode in alkaline fuel cells.
Stabilization of Lithium Metal Anodes by Hybrid Artificial Solid Electrolyte Interphase

Li metal is among the most attractive anode materials for secondary batteries, with a theoretical specific capacity > 3800 mAh g–1. However, its extremely low electrochemical potential is associated with high chemical reactivity that results in undesirable reduction of electrolyte species on the lithium surface, leading to spontaneous formation of a solid electrolyte interphase (SEI) with uncontrolled composition, morphology, and physicochemical properties. Here, we demonstrate a new approach to stabilize Li metal anodes using a hybrid organic/inorganic artificial solid electrolyte interphase (ASEI) deposited directly on the Li metal surface by self-healing electrochemical polymerization (EP) and atomic layer deposition (ALD). This hybrid protection layer is thin, flexible, ionically conductive, and electrically insulating. We show that Li metal protected by the hybrid protection layer gives rise to very stable cycling performance for over 300 cycles at current density 1 mA/cm2 and over 110 cycles at curr.