Miracle-dz/UniFAR-FTUs huggingface dataset:
Raising Animals Without Antibiotics: U.S. Producer and Veterinarian Experiences and Opinions

Ensuring the safety, health, and overall well-being of animals raised for food is both an ethical obligation and a critical component of providing safe food products. The use of antibiotics for maintaining animal health has come under scrutiny in recent years due to the rise of antibiotic resistance globally. Some U.S. producers, especially in the poultry industry, have responded by eliminating their antibiotic use. The number of animals raised without antibiotics (RWA) is growing in the U.S., but there are concerns that RWA practices might negatively impact animal health and welfare. Therefore, the objective of this study was to survey U.S. veterinarians and producers about their experiences and opinions regarding RWA production. Veterinarians, farmers, ranchers, producers, and other stakeholders involved in raising broilers, turkeys, swine, beef cattle or dairy cattle were surveyed. Of the 565 completed responses received, 442 self-reported as practicing veterinarians or producers. Just over half of respondents reported having past or current experience with RWA programs. The main indicated reasons for raising animals without antibiotics were market driven; switching to RWA production was less commonly made for health-related reasons, such as to reduce antibiotic resistance or to improve animal health and welfare. Although respondents felt that RWA production has negative impacts on animal health and welfare, they overwhelmingly (>70%) indicated that the customer (retailer/restaurant/food service) believes that animal and health welfare will be significantly improved. Veterinarians and producers indicated that RWA programs will increase production costs with questionable effect on meat, egg or dairy consumer demand. Many respondents felt that there are times when the RWA label takes priority over animal health and welfare. Respondents generally felt that there was a need for increased auditing/assessment of animal health and welfare in RWA systems.
Frin: An Efficient Method for Representing Genome Evolutionary History

Phylogenetic analysis is important in understanding the process of biological evolution, and phylogenetic trees are used to represent the evolutionary history. Each taxon in a phylogenetic tree has not more than one parent, so phylogenetic trees cannot express the complex evolutionary information implicit in phylogeny. Phylogenetic networks can be used to express genome evolutionary histories. Therefore, it is great significance to research the construction of phylogenetic networks. Cass algorithm is an efficient method for constructing phylogenetic networks because it can construct a much simpler network. However, Cass relies heavily on the order of input data, i.e. different networks can be constructed for the same dataset with different input orders. Based on the frequency and incompatibility degree of taxa, we propose an efficiently improved algorithm of Cass, called as Frin. The experimental results show that the networks constructed by Frin are not only simpler than those constructed by other methods, but Frin can also construct more consistent phylogenetic networks when the treated data have different input orders. Furthermore, the phylogenetic network constructed by Frin is closer to the original information described by phylogenetic trees. Frin has been built as a Java software package and is freely available at https://github.com/wangjuanimu/Frin.
Early Cognitive and Behavioral Deficits in Mouse Models for Tauopathy and Alzheimer’s Disease

Neurocognitive disorders, among which Alzheimer’s disease (AD), have become one of the major causes of death in developed countries. No effective disease-modifying therapy is available, possibly because current treatments are administered too late to still be able to intervene in the disease progress. AD is characterized by a gradual onset with subclinical neurobiological and behavioral changes that precede diagnosis with years to even decades. The earlier the diagnosis, the earlier potential treatments can be tested and started. Mouse models are valuable to study the possible causes underlying early phases of neuropathology and their reflection in behavior and other biomarkers, to help improve preclinical detection and diagnosis of AD. Here, we assessed cognitive functioning and social behavior in transgenic mice expressing tau pathology only (Tau-P301L) or a combination of amyloid and tau pathology [amyloid precursor protein (APP)-V717I × Tau-P301L]. The mice were subjected to a variety of behavioral tasks at an age of 3–6 months, i.e., at an early phase of their AD-like pathology. We hypothesized that compared to age-matched wild-type controls, transgenic mice would show specific impairments in both cognitive and non-cognitive tasks. In line with our expectations, transgenic mice showed decreased cognitive flexibility in the Morris water maze, decreased exploratory behavior, decreased performance in a nesting task, and increased anxiety-like behavior. In accordance with the amyloid-cascade hypothesis, some of the behavioral measures showed more severe deficits in APP-V717I × Tau-P301L compared to Tau-P301L mice, indicating an exacerbation of disease processes due to the co-occurrence of amyloid and tau pathology. Our study supports the use of behavioral markers as early indicators of ongoing AD pathology during the preclinical phase.
Antifungal Activity, Toxicity, and Membranolytic Action of a Mastoparan Analog Peptide

Invasive fungal infections, such as cryptococcosis and paracoccidioidomycosis are associated with significant rates of morbidity and mortality. Cryptococcosis, caused by Cryptococcus neoformans, is distributed worldwide and has received much attention as a common complication in patients with HIV. Invasive fungal infections are usually treated with a combination of amphotericin B and azoles. In addition, 5-fluorocytosine (5-FC) is applied in cryptococcosis, specifically to treat central nervous system infection. However, host toxicity, high cost, emerging number of resistant strains, and difficulty in developing new selective antifungals pose challenges. The need for new antifungals has therefore prompted a screen for inhibitory peptides, which have multiple mechanisms of action. The honeycomb moth Galleria mellonella has been widely used as a model system for evaluating efficacy of antifungal agents. In this study, a peptide analog from the mastoparan class of wasps (MK58911) was tested against Cryptococcus spp. and Paracoccidioides spp. In addition, peptide toxicity tests on lung fibroblasts (MRC5) and glioblastoma cells (U87) were performed. Subsequent tests related to drug interaction and mechanism of action were also performed, and efficacy and toxicity of the peptide were evaluated in vivo using the G. mellonella model. Our results reveal promising activity of the peptide, with an MIC in the range of 7.8–31.2 μg/mL, and low toxicity in MRC and U87 cells (IC50 > 500 μg/mL). Taken together, these results demonstrate that MK58911 is highly toxic in fungal cells, but not mammalian cells (SI > 16). The mechanism of toxicity involved disruption of the plasma membrane, leading to death of the fungus mainly by necrosis. In addition, no interaction with the drugs amphotericin B and fluconazole was found either in vitro or in vivo. Finally, the peptide showed no toxic effects on G. mellonella, and significantly enhanced survival rates of larvae infected with C. neoformans. Although not statistically significant, treatment of larvae with all doses of MK58911 showed a similar trend in decreasing the fungal burden of larvae. These effects were independent of any immunomodulatory activity. Overall, these results present a peptide with potential for use as a new antifungal drug to treat systemic mycoses.
Reactivity to Measures of Metacognition

Metacognition is typically measured by collecting self-reported information from participants while they complete a cognitive task. Recent evidence suggests that eliciting such metacognitive information from participants can impact both their metacognitive processes and their cognitive performance. Although there are contradictory findings regarding the magnitude and even the direction of this effect, recent evidence has converged to provide a clearer picture of the mechanisms that determine reactivity. Here, we provide a review of the evidence that measures of metacognition, namely think-aloud protocols, judgments of learning, and confidence ratings, are reactive. We argue that reactivity has important implications not just for the measurement of metacognition, but for metacognition theorizing because reactivity can provide insights into the cues participants use to monitor their performance. Drawing from this synthesis of evidence, we propose a tentative framework for studying reactivity that integrates cue processing accounts of reactivity with existing models of metacognition. We conclude the review by addressing some of the pertinent questions yet to be comprehensively addressed by reactivity research, including how researchers should best address issues of reactivity when using experimental designs.
HSV-2 Cellular Programming Enables Productive HIV Infection in Dendritic Cells

Genital herpes is a common sexually transmitted infection caused by herpes simplex virus type 2 (HSV-2). Genital herpes significantly enhances the acquisition and transmission of HIV-1 by creating a microenvironment that supports HIV infection in the host. Dendritic cells (DCs) represent one of the first innate cell types that encounter HIV-1 and HSV-2 in the genital mucosa. HSV-2 infection has been shown to modulate DCs, rendering them more receptive to HIV infection. Here, we investigated the potential mechanisms underlying HSV-2-mediated augmentation of HIV-1 infection. We demonstrated that the presence of HSV-2 enhanced productive HIV-1 infection of DCs and boosted inflammatory and antiviral responses. The HSV-2 augmented HIV-1 infection required intact HSV-2 DNA, but not active HSV-2 DNA replication. Furthermore, the augmented HIV infection of DCs involved the cGAS-STING pathway. Interestingly, we could not see any involvement of TLR2 or TLR3 nor suppression of infection by IFN-β production. The conditioning by HSV-2 in dual exposed DCs decreased protein expression of IFI16, cGAS, STING, and TBK1, which is associated with signaling through the STING pathway. Dual exposure to HSV-2 and HIV-1 gave decreased levels of several HIV-1 restriction factors, especially SAMHD1, TREX1, and APOBEC3G. Activation of the STING pathway in DCs by exposure to both HSV-2 and HIV-1 most likely led to the proteolytic degradation of the HIV-1 restriction factors SAMHD1, TREX1, and APOBEC3G, which should release their normal restriction of HIV infection in DCs. This released their normal restriction of HIV infection in DCs. We showed that HSV-2 reprogramming of cellular signaling pathways and protein expression levels in the DCs provided a setting where HIV-1 can establish a higher productive infection in the DCs. In conclusion, HSV-2 reprogramming opens up DCs for HIV-1 infection and creates a microenvironment favoring HIV-1 transmission.
Evaluation of CORDEX Regional Climate Models in Simulating Extreme Dry Spells in Southwest China

In recent decades, Southwest China (SWC) has experienced a series of severe and extensive droughts resulting in tremendous socioeconomic losses. The annual maximum dry spell length (AMDSL), which refers to the number of consecutive days without rainfall, or days with rainfall below a threshold, plays an important role in triggering drought. The main objective of this study is to provide a comparison of the capabilities of current regional climate models (RCMs) in simulating extreme dry spell characteristics in mountainous SWC. Five available RCM simulations utilized in the Coordinated Regional Climate Downscaling Experiment (CORDEX)-East Asia project over 1981 to 2005 were employed in this study; the RCMs being NIMR-HadGEM3, SNU-MM5, SNU-WRF, KNU-RegCM4 and YSU-RSM. Firstly, it was found that all RCMs reasonably simulate the main seasonality features of rainfall and dry days in SWC. Furthermore, besides YSU-RSM, the other four RCMs can accurately capture the spatial pattern of dry-day occurrence based on Taylor diagram diagnosis. Secondly, we assessed the performance of five RCMs to detect and reproduce the climatology and variability of the AMDSL. In general, RCMs simulate the spatial pattern of long-term mean and interannual variability of the AMDSL in SWC well. Based on Taylor diagram evaluation, NIMR-HadGEM3 was the best among 5 RCMs in simulating the AMDSL characteristics. Thirdly, the generalized extreme value (GEV) distribution is considered the most suitable model fitting the AMDSL in both observation and RCM experimental data in comparison to other three-parameter probabilistic models. Higher value centers of the scale parameter and the location parameter indicate a wider and amplified distribution of the AMDSL over the low-latitude highlands (LLH) region against other areas in Southwest China, which is consistent with spatial patterns of climatological AMDSL. In addition, sensitivity analysis of different thresholds for dry days show that the 1 mm threshold is suitable for this study and different threshold choices have little effect on simulation ability.
Assessing, Monitoring and Analyzing Linked Data Quality in Public SPARQL Endpoints

In this paper, we propose a domain agnostic and query driven approach to monitor, assess, and analyze quality of the linked data hosted by public SPARQL endpoints. We identiﬁed various quality related metrics for linked datasets and used linked data vocabulary to represent quality information. We provide a Linked Data Quality (LDQ) dataset, which is generated after conducting various quality related tests over a few public SPARQL endpoints. Our main goal in this paper is to provide a platform for monitoring, assessing and analyzing linked data quality. Data consumers can also execute various analytical queries over LDQ to analyze quality related metrics of the public SPARQL endpoints. We hope that LDQ will increase data consumer’s conﬁdence over public SPARQL endpoints and will support the wide adoption of these datasets in various linked data applications.
Neuroimaging Of Cold Allodynia Reveals A Central Disinhibition Mechanism Of Pain

Purpose Allodynia refers to pain evoked by physiologically innocuous stimuli. It is a disabling symptom of neuropathic pain following a lesion within the peripheral or central nervous system. In fact, two different pathophysiological mechanisms of cold allodynia (ie, hypersensitivity to innocuous cold) have been proposed. The peripheral sensitization of nociceptive neurons can produce cold allodynia, which can be induced experimentally by a topical application of menthol. An alternative mechanism involves reduced inhibition of central pain processing by innocuous cold stimuli. A model to induce the latter type of allodynia is the conduction block of peripheral A-fiber input. Patients and methods In the presented study, functional MRI was used to analyze these two different experimental models of cold allodynia. In order to identify the underlying cerebral activation patterns of both mechanisms, the application of menthol and the induction of a mechanical A-fiber blockade were studied in healthy volunteers. Results The block-induced cold allodynia caused significantly stronger activation of the medial polymodal pain processing pathway, including left medial thalamus, anterior cingulate cortex, and medial prefrontal cortex. In contrast, menthol-induced cold allodynia caused significantly stronger activity of the left lateral thalamus as well as the primary and secondary somatosensory cortices, key structures of the lateral discriminative pathway of pain processing. Mean pain intensity did not differ between both forms of cold allodynia. Conclusion Experimental cold allodynia is mediated in different cerebral areas depending on the underlying pathophysiology. The activity pattern associated with block-induced allodynia confirms a fundamental integration between painful and non-painful temperature sensation, ie, the cold-induced inhibition of cold pain.
Trichopolydesmidae from Cameroon, 2: A species-level reclassification of Afrotropical trichopolydesmids (Diplopoda, Polydesmida), with two new species and two new records from Cameroon, and two new species from the Nimba Mountains, Guinea

Abstract A revised classification of Afrotropical Trichopolydesmidae is presented. The fauna presently contains as many as 52 species in six recognized genera, with numerous new transfers/combinations involved: Bactrodesmus Cook, 1896 (3 species, including B. grandissp. nov. from the Nimba Mountains, Guinea), Eburodesmus Schubart, 1955 (2 species), Hemisphaeroparia Schubart, 1955 (26 species, including one old species, Polydesmus parvulus Porat, 1894, revised from type material and provisionally assigned to Hemisphaeroparia, as well as two new records and two new species from Cameroon: H. longibrachiatasp. nov. and H. avissp. nov.), Mecistoparia Brolemann, 1926 (3 species), Physetoparia Brolemann, 1920 (12 species, including P. complexasp. nov. from the Nimba Mountains, Guinea), and Sphaeroparia Attems, 1909 (6 species). The hitherto enigmatic genus Bactrodesmus is redefined, but the monotypic Trichozonus Carl, 1905 still remains dubious.
Linc00511 Indicates A Poor Prognosis Of Liver Hepatocellular Carcinoma

Objective To uncover the specific function of linc00511 in the progression of liver hepatocellular carcinoma (LIHC) and the underlying mechanism. Patients and methods GEPIA dataset containing 9736 LIHC samples and 857 normal samples were downloaded from TCGA. Expression pattern and prognostic potential of linc00511 in LIHC were analyzed. Subsequently, expression level of linc00511 in LIHC tissues collected in our hospital and cell lines were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Differential expressions of linc00511 in LIHC with different tumor grades and metastatic status were compared. After transfection of si-linc00511, proliferative and migratory changes in Huh7 and Hep3B cells were assessed by cell counting kit-8 (CCK-8), 5-ethynyl-2ʹ-deoxyuridine (EdU) and Transwell assay. Lastly, Pearson correlation analysis and qRT-PCR were conducted to investigate the interaction between linc00511 and miR-29c. Results Linc00511 was upregulated in LIHC tissues and cell lines. Its level was positively correlated to TNM staging, lymphatic metastasis and poor prognosis in LIHC patients. Knockdown of linc00511 attenuated proliferative and migratory abilities in Huh7 and Hep3B cells. In addition, miR-29c was downregulated in LIHC and negatively linked to linc00511 level. A negative interaction between linc00511 and miR-29c could be a regulatory feedback influencing the progression of LIHC. Conclusion Linc00511 accelerates the proliferation and migration in LIHC, thus aggravating tumor progression. Meanwhile, linc00511 could be utilized as a hallmark predicting poor prognosis in LIHC patients.
Estrogen Receptor Beta Inhibits The Proliferation, Migration, And Angiogenesis Of Gastric Cancer Cells Through Inhibiting Nuclear Factor-Kappa B Signaling

Purpose This study aimed to investigate the regulatory roles of estrogen receptor beta (ERβ) on gastric cancer (GC) cells, and reveal the potential mechanisms relating to nuclear factor-kappa B (NF-κB) signaling. Methods GC cell lines SGC7901 and MKN45 were transfected with pEGFP-C1-ERβ to overexpress ERβ, and treated with PMA (a NF-κB activator) to activate NF-κB signaling. The cell proliferation and migration, as well as the formation of vessel-like structures in human venous endothelial cells (HUVECs) were detected. The expression of ERβ, NF-κB p65, p-NF-κB p65, Ki67 (a proliferation marker), vascular endothelial growth factor A (VEGF-A) and matrix metalloproteinase 2 (MMP-2), the DNA binding activity of NF-κB p65, the content of VEGF-A, and the activity of MMP-2 were detected in SGC7901 and MKN45 cells. Results The transfection of pEGFP-C1-ERβ significantly increased the expression of ERβ in SGC7901 and MKN45 cells (P < 0.05). Overexpression of ERβ in SGC7901 and MKN45 cells significantly decreased the cell activity, cell number in G2/M phase, cell migration, the expression of Ki67, VEGF-A and MMP-2, VEGF-A content, MMP-2 activity, as well as the number of vessel-like structures formed by HUVECs (P < 0.05). Overexpression of ERβ also significantly decreased the DNA binding activity and the expression of p-NF-κB p65 in SGC7901 and MKN45 cells (P < 0.05). The anti-tumor effect of ERβ overexpression on GC cells was reversed by the intervention of PMA (P < 0.05). Conclusion Overexpression of ERβ inhibited the proliferation, migration, and angiogenesis of GC cells through inhibiting NF-κB signaling.
Expedited Removal of a Radial Hemostatic Compression Device Following Cardiac Catheterization Is Safe and Associated With Reduced Time to Discharge

Background Radial access for cardiac catheterization has become increasingly adopted, owing much of its popularity to decreased bleeding complications compared with the femoral approach. Hemostatic compression devices (HCDs) for radial catheterization play a key role in this advantage, but the optimal duration of compression is unknown. A shorter duration of compression is encouraged by guidelines, but removing an HCD too quickly could result in serious bleeding. We aimed to evaluate the safety and effectiveness of expedited removal of a radial HCD after cardiac catheterization. Methods We conducted a prospective study of patients undergoing radial cardiac catheterization and/or percutaneous coronary intervention at a tertiary care academic medical center. Patients underwent HCD application using a TR Band® (Terumo Interventional Systems) which was removed after a prespecified amount of time in each of three sequential temporal cohorts: 2-h, 1-h, or 0.5-h. Each patient was monitored for development of bleeding or hematoma and for serious complications. Results A total of 354 patients participated in our study, with similar numbers in each group. There was a greater rate of minor bleeding in the 0.5-h (12%) and 1-h (19%) groups compared with the 2-h group (8%), but there were no serious complications (need for surgical consultation, transfusion, or unplanned admission) in any group. The average time to discharge was shorter in the 0.5-h and 1-h groups compared with the 2-h group. Conclusions Deflating the radial HCD at 0.5 h is safe with no increase in the observed rate of major complications and is associated with reduced time to discharge after coronary angiography or percutaneous coronary intervention using the radial arterial approach.