Miracle-dz/UniFAR-FTUs huggingface dataset:
Porcine LIF gene polymorphisms and their association with litter size traits in four pig breeds

Abstract: Leukemia inhibitory factor (LIF) is an important productivity-related gene in pigs. We found two polymorphisms — g.6646C>T and g.6988C>T — in exon 3 of LIF in pigs by using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism. Three genotypes were obtained and associated with litter size traits in Anqing Six-end-white (AQ), Wei (W), Wannan Black (WNB), and Large White (LW) pigs. At locus g.6646C>T, the g.6646C allele frequency variation was 0.6869 (AQ), 0.7473 (W), 1 (WNB), and 0.6852 (LW). In AQ pigs, sows with the TT genotype had higher total number of piglets born (TNB) and number of piglets born alive (NBA) in the first parity and multiparities (P < 0.01). In W and LW pigs, sows with the CC genotype had higher TNB and NBA in multiparities (P < 0.01). At locus g.6988C>T, the g.6988C allele frequency variation was 1 (AQ), 0.6154 (W), 1 (WNB), and 0.6667 (LW). The CC genotype significantly differed from CT or TT genotypes (P < 0.01) for TNB and NBA in W and LW pigs. Thus, LIF was shown to have a significant influence on litter size. Therefore, g.6646C>T and g.6988C>T loci of LIF could be potential marker-assisted selection tools for improving litter size in pig production.
Orientations without forbidden patterns on three vertices

Given a set of oriented graphs $F$, a graph $G$ is an $F$-graph if it admits an $F$-free orientation. Building on previous work by Bang-Jensen and Urrutia, we propose a master algorithm that determines if a graph admits an $F$-free orientation when $F$ is a subset of the orientations of $P_3$ and the transitive triangle. We extend previous results of Skrien by studying the class of $F$-graphs, when $F$ is any set of oriented graphs of order three; structural characterizations for all such sets are provided, except for the so-called perfectly-orientable graphs and one of its subclasses, which remain as open problems.
The Cytoprotective Enzyme Heme Oxygenase-1 Suppresses Pseudorabies Virus Replication in vitro

Pseudorabies virus (PRV) infection brings about great economic losses to the swine industry worldwide, as there are currently no effective therapeutic agents or vaccines against this disease, and mutations in endemic wild virulent PRV strains result in immune failure of traditional vaccines. Heme oxygenase-1 (HO-1) catalyzes the conversion of heme into biliverdin (BV), iron and carbon monoxide (CO), all of which have been demonstrated to protect cells from various stressors. However, the role of HO-1 in PRV replication remains unknown. Thus, the present study aimed to investigate the effect of HO-1 on PRV replication and determine its underlying molecular mechanisms. The results demonstrated that induction of HO-1 via cobalt-protoporphyrin (CoPP) markedly suppressed PRV replication, while HO-1 specific small interfering RNA or inhibitor zinc-protoporphyrin partially reversed the inhibitory effect of CoPP on PRV replication. Furthermore, overexpression of HO-1 notably inhibited PRV replication, while knockdown of endogenous HO-1 expression promoted PRV replication. Mechanism analyses indicated that the HO-1 downstream metabolites, CO and BV/BR partially mediated the virus suppressive effect of HO-1. Taken together, the results of the present study suggest that HO-1 may be developed as a novel endogenous antiviral factor against PRV, and the HO-1/BV/CO system may constitute a unique antiviral protection network during PRV infection and interaction with host cells.
Tumor Mutational Burden Determined by Panel Sequencing Predicts Survival After Immunotherapy in Patients With Advanced Gastric Cancer

Objective: Panel-based sequencing is widely used to measure tumor mutational burden (TMB) in clinical trials and is ready to enter routine diagnostics. However, cut-off points to distinguish “TMB-high” from “TMB-low” tumors are not consistent and the clinical implications of TMB in predicting responses to immune checkpoint blockade (ICB) in gastric cancer are not clearly defined. We aimed to assess whether TMB is associated with the response to immunotherapy and to examine its relation with other biomarkers of immunotherapy response in advanced gastric cancer. Design: In total, 63 patients with advanced gastric cancer treated with ICB were included in the study. Panel-based TMB in gastric tumor samples, treatment responses to ICB, clinicopathological data, and time to progression were retrospectively analyzed. Microsatellite instability (MSI) status, Epstein–Barr virus (EBV) positivity, and programmed death-ligand 1 (PD-L1) combined positive score (CPS) were also analyzed. Results: TMB ranged from 0 to 446 mutations/megabase (mt/mb) and was significantly associated with MSI (P < 0.001), PD-L1 CPS (P = 0.022), response to ICB (P = 0.04), chemotherapy (P = 0.02) and older patient age (≥65 years; P = 0.0014). The cut-off point of 14.31 mt/mb determined by log-rank statistics for progression-free survival divided the tumors into eight (12.7%) TMB-high and 55 (87.3%) TMB-low tumors. The median TMB of the chemo-refractory group was significantly higher (8.43 mt/mb) compared to that of chemo-naïve group (3.42 mt/mb) (P = 0.02). Patients with TMB-high tumors showed prolonged progression-free survival in univariate [HR, 0.32; 95% confidence interval (CI), 0.12–0.90] and multivariate (HR, 0.21; 95% CI, 0.07–0.69) analyses. In area under the receiver operating curve (AUC) analysis of TMB, PD-L1, EBV, MSI, and their combination, the AUC value was the highest for EBV (0.97), followed by MSI (0.96), PD-L1 (0.81), the combination (0.78), and TMB (0.56). Conclusion: In addition to EBV, MSI, and PD-L1 CPS, TMB could be used as a predictive biomarker in patients with advanced gastric cancer treated with ICB and may aid clinical decision making.
Child And Adolescent Psychiatry A Comprehensive Textbook

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Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation

Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not only yield but also development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies, emmer (Triticum turgidum ssp. dicoccum) and durum wheat (Triticum turgidum ssp. durum). We found that durum wheat exhibits broader and stronger response in comparison to emmer as evidenced by the analysis of the differential expression pattern of both genes and metabolites and gene enrichment analysis. Emmer and durum wheat showed major differences in the responses to N starvation for transcription factor families. While emmer showed differential reduction in the levels of primary metabolites to N starvation, durum wheat exhibited increased levels of most metabolites, including GABA as an indicator of metabolic imbalance. The correlation-based networks including the differentially expressed genes and metabolites revealed tighter regulation of metabolism in durum wheat in comparison to emmer, as evidenced by the larger number of significant correlations. We also found that glutamate and GABA had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and Glutamate signaling modulating shoot vs root growth in the two different wheat subspecies.
Poly(vinyl pyrrolidone)-modified metal oxide anode interlayers for stable organic solar cells

Abstract. A new generation of anode interlayers (AILs) has been introduced in recent years for improving the efficiency and stability of organic solar cell (OSC) devices. Electrode interlayer modification is a simple and effective way of enhancing OSC device performance. We used poly(vinyl pyrrolidone) (PVP) as an AIL modifier to alter molybdenum trioxide (MoO3) and vanadium pentoxide (V2O5) AILs in OSC devices and compared them with pure metal oxide AILs. Using this modification, average power conversion efficiencies were raised from 5.2 % ± 0.4 % to 6.0 % ± 0.3 % for OSCs with MoO3-based AILs, and from 6.2 % ± 0.1 % to 6.8 % ± 0.3 % for OSCs with V2O5-based AILs. Moreover, the PVP-metal oxide AILs also improved the overall device quality, producing a nanotextured morphology with good optical properties and favorable chemical composition. Beneficial wetting properties for interfacial adhesion between anode and active layer are observed using contact angle measurements. Overall, devices with PVP-modified metal oxide AILs showed promising results with greater device stability compared to pure metal oxide AIL-based OSC devices.
ELECTORAL SYSTEMS AND INTERNATIONAL TRADE POLICY

We develop a simple theoretic game a model to analyze the relationship between electoral sys tems and governments' choice in trade policies. We show that existence of international pressure or foreign lobby changes a government's final decision on trade policy, and trade policy in countries with proportional electoral system is more protectionist than in countries with majoritarian electoral system. Moreover, lobbies pay more to affect the trade policy outcomes in countries with proportional representation systems.
SMap: Internet-wide Scanning for Ingress Filtering

To protect from attacks, networks need to enforce ingress filtering. Despite the importance, the existing studies do not allow to infer the extent of ingress filtering at Internet-scale, providing results with only a limited coverage: they can either measure networks that operate servers with faulty network-stack implementations, or require installation of the measurement software by volunteers, or assume specific properties, like traceroute loops, which are challenging to reproduce in practice. Improving coverage of the spoofing measurements is critical. In this work we present the Spoofing Mapper (SMap): the first scanner for performing Internet-wide studies of enforcement of ingress filtering. The SMap measurement methodology utilises standard protocols' behaviour that are present in almost any network. SMap not only provides better coverage of ingress-filtering measurements, but it is also more effective than the previous approaches. We applied SMap for Internet-wide measurements: we found that 21% of all the Autonomous Systems (ASes) in the Internet do not filter spoofed packets, in contrast to 2.5% ASes identified by the most recent study with volunteers (of the Spoofer Project), as well as 13173 new spoofable ASes, which were not detected by the other tools. Our study with SMap provides the most comprehensive view of ingress filtering deployment in the Internet and remediation in filtering spoofed packets over a period of six months until February 2020. SMap is simple to use and does not require installation on the tested network nor coordination with the tested networks. We set up a web service at http://to_be_revealed/ which reports statistics from SMap evaluations and enables continual Internet-wide data collection and analysis. We also make our datasets as well as the SMap tool publicly available to enable researchers to reproduce and validate the results.
P2 Receptors as Therapeutic Targets in the Salivary Gland: From Physiology to Dysfunction

Although often overlooked in our daily lives, saliva performs a host of necessary physiological functions, including lubricating and protecting the oral cavity, facilitating taste sensation and digestion and maintaining tooth enamel. Therefore, salivary gland dysfunction and hyposalivation, often resulting from pathogenesis of the autoimmune disease Sjögren’s syndrome or from radiotherapy of the head and neck region during cancer treatment, severely reduce the quality of life of afflicted patients and can lead to dental caries, periodontitis, digestive disorders, loss of taste and difficulty speaking. Since their initial discovery in the 1970s, P2 purinergic receptors for extracellular nucleotides, including ATP-gated ion channel P2X and G protein-coupled P2Y receptors, have been shown to mediate physiological processes in numerous tissues, including the salivary glands where P2 receptors represent a link between canonical and non-canonical saliva secretion. Additionally, extracellular nucleotides released during periods of cellular stress and inflammation act as a tissue alarmin to coordinate immunological and tissue repair responses through P2 receptor activation. Accordingly, P2 receptors have gained widespread clinical interest with agonists and antagonists either currently undergoing clinical trials or already approved for human use. Here, we review the contributions of P2 receptors to salivary gland function and describe their role in salivary gland dysfunction. We further consider their potential as therapeutic targets to promote physiological saliva flow, prevent salivary gland inflammation and enhance tissue regeneration.
The Influence of Device Type on Querying Behavior and Learning Outcomes in a Searching as Learning Task with a Laptop or Smartphone

In this study we examined the influence of device type (i.e., laptop vs. smartphone) on N = 49 secondary-school students' search query length and number of queries used in a Searching as Learning (SAL) task addressing a controversial socio-scientific issue (i.e., the use of nuclear power to solve the climate crisis). Furthermore, we examined the influence of device type on students' learning outcomes by analyzing the number of pro and con arguments included in a subsequent essay task. Results showed that on laptops students used more queries than on smartphones. In contrast, no differences were found in search query length or in the number of pro and con arguments in the essay. Moreover, irrespective of device type, average search query length was positively associated with the number of con arguments. To conclude, the present study provides first indications that smartphone usage could be incorporated in the classroom for Web inquiry tasks.
Ensemble Detection and Analysis of Communities in Complex Networks

Though much work has been done on ensemble clustering in data mining, the application of ensemble methods to community detection in networks is in its infancy. In this article, we propose MeDOF, an ensemble method which performs disjoint, overlapping, and fuzzy community detection and represents one of the first ever ensemble methods for fuzzy and overlapping community detection. We run extensive experiments on both synthetic and several real-world datasets for which community structures are known. We show that MeDOF beats the best-known existing stand-alone community detection algorithms. We further show that MeDOF can help explore core-periphery structure of network communities, identify stable communities in dynamic networks, and help solve the “degeneracy of solutions” problem, generating robust results.
Discovery of extended structures around two evolved planetary nebulae M2–55 and Abell 2

We report a multi-wavelength study of two evolved planetary nebulae (PNs) M 2-55 and Abell 2. Deep optical narrow-band images ([O III], H? , and [N II]) of M 2-55 reveal two pairs of bipolar lobes and a new faint arc-like structure. This arc-shaped filament around M 2-55 appears a well-defined boundary from southwest to southeast, strongly suggesting that this nebula is in interaction with its surrounding interstellar medium. From the imaging data of Wide-field Infrared Survey Explorer (WISE) all-sky survey, we discovered extensive mid-infrared halos around these PNs, which are approximately twice larger than their main nebulae seen in the visible. We also present a mid-resolution optical spectrum of M 2-55, which shows that it is a high-excitation evolved PN with a low electron density of 250 cm^-3. Furthermore, we investigate the properties of these nebulae from their spectral energy distributions (SEDs) by means of archival data.
Altered Tregs Differentiation and Impaired Autophagy Correlate to Atherosclerotic Disease

Atherosclerosis is a progressive vascular disease representing the primary cause of morbidity and mortality in developed countries. Formerly, atherosclerosis was considered as a mere passive accumulation of lipids in blood vessels. However, it is now clear that atherosclerosis is a complex and multifactorial disease, in which the involvement of immune cells and inflammation play a key role. A variety of studies have shown that autophagy—a cellular catalytic mechanism able to remove injured cytoplasmic components in response to cellular stress—may be proatherogenic. So far, in this context, its role has been investigated in smooth muscle cells, macrophages, and endothelial cells, while the function of this catabolic protective process in lymphocyte functionality has been overlooked. The few studies carried out so far, however, suggested that autophagy modulation in lymphocyte subsets may be functionally related to plaque formation and development. Therefore, in this research, we aimed at better clarifying the role of lymphocyte subsets, mainly regulatory T cells (Tregs), in human atherosclerotic plaques and in animal models of atherosclerosis investigating the contribution of autophagy on immune cell homeostasis. Here, we investigate basal autophagy in a mouse model of atherosclerosis, apolipoprotein E (ApoE)-knockout (KO) mice, and we analyze the role of autophagy in driving Tregs polarization. We observed defective maturation of Tregs from ApoE-KO mice in response to tumor growth factor-β (TGFβ). TGFβ is a well-known autophagy inducer, and Tregs maturation defects in ApoE-KO mice seem to be related to autophagy impairment. In this work, we propose that autophagy underlies Tregs maturation, advocating that the study of this process in atherosclerosis may open new therapeutic strategies.
Predicting Bystander Intention to Intervene: The Role of Gender-Specific System Justification and Rape Myth Acceptance for Men and Women

The relationship between rape myth acceptance, gender-specific system justification (GSJ), and bystander intention to intervene has often been studied on a one-dimensional basis, without separating the four dimensions of the acceptance of rape myths. The current study analyzes the relationship between the acceptance of rape myths, GSJ, and bystander intention to intervene, and explores whether the relationships operate differently for men and women. The sample was 3,966 university students: 2,962 from the University of Turin and 1,004 from the Politecnico of Turin; 71.2% women and 28.8% men; average age of 22.61 years. After descriptive analyses, independent sample T-test, and bivariate correlations, a model where the acceptance of four rape myths (“She asked for it”; “He didn’t mean to”; “It wasn’t really rape”; “She lied”) mediated the relationship between GSJ and bystander intention to intervene was tested on the whole sample and then separately on women and men. A bootstrapping procedure was applied. Our data show that for both men and women, GSJ was related to the four rape myths, whereas women and men differed on the relationship between acceptance of rape myths and bystander intention to intervene: only the dimension “She asked for it” was significant for both groups; the dimension “It wasn’t really rape” was significant only for the men. Focusing on the differences in women and men regarding acceptance of rape myths can be fruitful for a theoretical deepening of the field and may inform the development of more successful prevention programs.
Circadian Regulation of Immunity Through Epigenetic Mechanisms

The circadian clock orchestrates daily rhythms in many physiological, behavioral and molecular processes, providing means to anticipate, and adapt to environmental changes. A specific role of the circadian clock is to coordinate functions of the immune system both at steady-state and in response to infectious threats. Hence, time-of-day dependent variables are found in the physiology of immune cells, host-parasite interactions, inflammatory processes, or adaptive immune responses. Interestingly, the molecular clock coordinates transcriptional-translational feedback loops which orchestrate daily oscillations in expression of many genes involved in cellular functions. This clock function is assisted by tightly controlled transitions in the chromatin fiber involving epigenetic mechanisms which determine how a when transcriptional oscillations occur. Immune cells are no exception, as they also present a functional clock dictating transcriptional rhythms. Hereby, the molecular clock and the chromatin regulators controlling rhythmicity represent a unique scaffold mediating the crosstalk between the circadian and the immune systems. Certain epigenetic regulators are shared between both systems and uncovering them and characterizing their dynamics can provide clues to design effective chronotherapeutic strategies for modulation of the immune system.
Interspecific Signaling Between the Parasitic Plant and the Host Plants Regulate Xylem Vessel Cell Differentiation in Haustoria of Cuscuta campestris

The genus Cuscuta is stem parasitic angiosperms that parasitize a wide range of vascular plants via de novo formation of a distinctive parasitic organ called a haustorium. In the developing haustorium, meristematic cells, which are initiated from the stem cortical tissue, differentiate into haustorial parenchyma cells, which elongate, penetrate into the host tissues, and finally connect with the host vasculature. This interspecific vasculature connection allows the parasite to uptake water and nutrients from the host plant. Although histological aspects of haustorium development have been studied extensively, the molecular mechanisms underlying vasculature development and the interspecific connection with the host vasculature remain largely unknown. To gain insights into the interspecific cell-to-cell interactions involved in haustorium development, we established an in vitro haustorium induction system for Cuscuta campestris using Arabidopsis thaliana rosette leaves as the host plant tissue. The in vitro induction system was used to show that interaction with host tissue was required for the differentiation of parasite haustorial cells into xylem vessel cells. To further characterize the molecular events occurring during host-dependent xylem vessel cell differentiation in C. campestris, we performed a transcriptome analysis using samples from the in vitro induction system. The results showed that orthologs of genes involved in development and proliferation of vascular stem cells were up-regulated even in the absence of host tissue, whereas orthologs of genes required for xylem vessel cell differentiation were up-regulated only after some haustorial cells had elongated and contacted the host xylem. Consistent results were obtained by another transcriptome analysis of the haustorium development in C. campestris undergoing parasitization of an intact host plant. These findings suggest the involvement of host-derived signals in the regulation of non-autonomous xylem vessel differentiation and suggest that its connection to the host xylem during the haustorium development activates a set of key genes for differentiation into xylem vessel cells.