Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide identification of the PYL gene family and expression of PYL genes under abiotic stresses in Chinese cabbage

The family of pyrabactin resistance 1 (PYR1)/PYR1-like (PYL) regulatory components of ABA receptors (RCAR) play a vital role in the initial step of ABA signaling. To understand the expression mode of PYL genes in response to various abiotic stresses in Chinese cabbage ( Brassica rapa ssp. pekinensis ), the members of BrPYL gene family were first identified with the relevant bioinformatics software. And then, the relative expressions of identified BrPYLs after heat, cold, drought, and salt treatments for 0, 24, 48, and 72 h were determined via real-time quantitative PCR. Here, we identified 24 PYLs in the B. rapa genome. Based on the phylogenetic analysis, these BrPYL genes were divided into three classes and distributed on ten chromosomes in Chinese cabbage. Most of BrPYL genes in the same group have similar gene structures and intron numbers. There were seven genes ( BrPYL 5, BrPYL8 , BrPYL22 , BrPYL3 , BrPYL18 , BrPYL11 , and BrPYL21 ) from Group A with two introns and one gene ( BrPYL19 ) from Group D with one intron. Analysis of conserved motifs suggested that every group contained motif 2 containing the Polyketide_cyc2 domain. Subsequently, the prediction of cis -acting elements indicated that BrPYL genes had 5 stress-related elements and 5 hormone-related elements, among which the number of MYC (dehydration reaction) was the highest, suggesting that BrPYL genes could respond to hormones and abiotic stresses. Expression patterns under four abiotic stresses showed that the expressions of BrPYL4 , BrPYL11 , BrPYL21 , and BrPYL23 responded to these stresses at different time points. To conclude, we identified the BrPYL genes and build the BrPYLs expression mode in response to various abiotic stresses. This study provides a theoretical basis for stress-resistance breeding of Chinese cabbage.
New classification-oriented laparoscopic anatomical hepatectomy strategy for hepatocellular carcinoma invading two or more (sub)segments in the left lobe

With technological advances in laparoscopic hepatectomy and new navigation devices, such as ﬂ exible laparoscopic ultrasound probes, indocyanine green (ICG)- ﬂ uorescent imaging and three-dimensional imaging, laparoscopic segmentectomy (LS), which maximizes the preservation of the functional hepatic reserve and the possibility for future repeat hepatectomy while ensuring adequate surgical margins, has become a feasible alternative to hemihepatectomy for addressing hepatocellular carcinoma (HCC). [1,2] However, for a single HCC invading two or more (sub)segments in the left lobe, most surgeons automatically choose left hemihepatectomy (LH) without considering the tumor ’ s anatomical distribution due to the relatively smaller volume of the left lobe. In fact, 80% to 90% of HCC patients in China have underlying cirrhosis. [3] Studies have proven that approximately one-third of postoperative hepatic dysfunction or even failure in patients with cirrhosis is attributed to LH. [4,5] As a result, in the current era of minimally invasive surgery, a more precise algorithm is needed to guide the surgical strategies for HCC in the left lobe. Herein, we proposed a new classi ﬁ cation-oriented laparoscopic anatomical hepatectomy strategy for a single HCC invading two or more (sub) segments in the left lobe, termed the Wu ’ s classi ﬁ cation. A new classi ﬁ cation
Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport

The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.
The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response

The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
Changes in submaximal and maximal measures of cardio-respiratory fitness resulting from 6-days of mountain walking

ABSTRACT Trekking is a popular activity associated with cardiovascular benefits. The aim of the present study was to investigate changes in the submaximal heart rate, oxygen uptake, oxygen pulse, and blood lactate concentration associated with a 6-day mountain walk. Over a 12-year period, 134 male (age 21.0 ± 1.4 years) and 124 female undergraduates (age 20.8 ± 1.6 years) participated. Three days before the trek submaximal and maximal laboratory measures were made on participants walking on a motorized treadmill using a breath-by-breath system to measure oxygen uptake (VO2) during exercise. Oxygen uptake and heart rate were recorded during steady-state exercise at treadmill gradients 0, 4, 8, 12, and 16%. Measurements were made, at the same time of day, two days after the trek. There were significant improvements in both the walking economy and the relative exercise intensity (%VO2max) at submaximal treadmill gradients 0-16%. Post-trek, heart rate was lower while oxygen pulse was higher, at each treadmill gradient. There was a significant increase in the maximal oxygen uptake for men (+2.7%) and women (+2.9%). The results of the present study suggest that improvements in cardiorespiratory fitness are associated with a 6-day mountain walk with no sex difference in the exercise response.
Comparative efficacy of three synchronization protocols in anestrous goats (Capra hircus)

The goal of this experiment was to compare the effectiveness of three popular synchronization protocols, viz. ovsynch, double prostaglandin (PGF2? /PG) injections, and MAP (Medroxyprogesterone acetate) sponges, in anestrous goats. Twenty one non pregnant multiparous anestrous goats with an average body condition score (BCS = 2.5) were selected. After the last PG injection, all the goats were exposed to three fertile bucks. They were observed to be in standing estrus. For further confirmation of copulation, a vaginal cytology test was performed for the presence of sperm inside the vaginal smear. Serum estradiol (E2) peaks were also estimated by using radioimmunoassay in estrus goats. MAP sponge efficiency with respect to estrus induction was found to be superior (57%) as compared to the rest (Ovsynch14 and PG 0%) (p< 0.05). Post PG standing estrus time in ovsynch and MAP groups was recorded as 48 h and 44 ± 12 h, respectively. The double PG group totally failed to show standing estrus. E2 peak levels ranging from 11-38 pg/ml in ovsynch and 10–25 pg/ml in the MAP group were observed in estrus goats. This study found the MAP sponge protocol most efficient for inducing estrus in anestrous goats.
A Proteomic Approach Reveals That miR-423-5p Modulates Glucidic and Amino Acid Metabolism in Prostate Cancer Cells

Recently, we have demonstrated that miR-423-5p modulates the growth and metastases of prostate cancer (PCa) cells both in vitro and in vivo. Here, we have studied the effects of miR-423-5p on the proteomic profile in order to identify its intracellular targets and the affected pathways. Applying a quantitative proteomic approach, we analyzed the effects on the protein expression profile of miR-423-5p-transduced PCa cells. Moreover, a computational analysis of predicted targets of miR-423-5p was carried out by using several target prediction tools. Proteomic analysis showed that 63 proteins were differentially expressed in miR-423-5-p-transfected LNCaP cells if compared to controls. Pathway enrichment analysis revealed that stable overexpression of miR-423-5p in LNCaP PCa cells induced inhibition of glycolysis and the metabolism of several amino acids and a parallel downregulation of proteins involved in transcription and hypoxia, the immune response through Th17-derived cytokines, inflammation via amphorin signaling, and ion transport. Moreover, upregulated proteins were related to the S phase of cell cycle, chromatin modifications, apoptosis, blood coagulation, and calcium transport. We identified seven proteins commonly represented in miR-423-5p targets and differentially expressed proteins (DEPs) and analyzed their expression and influence on the survival of PCa patients from publicly accessible datasets. Overall, our findings suggest that miR-423-5p induces alterations in glucose and amino acid metabolism in PCa cells paralleled by modulation of several tumor-associated processes.
Domains of operator semi-attraction of probability measures on Banach spaces

The paper deals with operator (semi-) stability and domains of operator (semi-) attraction of probability measures on infinite dimensional Banach spaces: characterizations of operator (semi-) stability and of domains of (normal) operator (semi-) attraction are given; it is shown that the set of operator stable probability measures is a closed subset under weak topology; the domain of operator semi-attraction of a given stable probability measure coincides with its domain of operator attraction; and a probability measure is (semi-) stable iff its finite-dimensional projections are (semi-) stable.
The aliasing‐phenomenon in visual terms

In a recent paper it was shown that the aliasing phenomenon, which leads to a severe identification problem in the estimation of stochastic differential equations, can be overcome by using a polygonal (or higher) approximation for the time paths of the exogenous variables. This work attempts to visualize the problem and presents several simulated trajectories of a continuous time AR(2)‐process (Ornstein‐Uhlenbeck‐process) together with the observationally equivalent structures. Furthermore it is shown that aliasing can even change the analytical properties of the time paths of the system: whereas the first component of the Ornstein‐Uhlenbeck‐process is differentiable, the trajectories of the aliasing structures are continuous, but not differentiable any more.
Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

Tea plants are widely grown all over the world because they are an important economic crop. The purity and authenticity of tea varieties are frequent problems in the conservation and promotion of germplasm resources in recent years, which has brought considerable inconvenience and uncertainty to the selection of parental lines for breeding and the research and cultivation of superior varieties. However, the development of core SNP markers can quickly and accurately identify the germplasm, which plays an important role in germplasm identification and the genetic relationship analysis of tea plants. In this study, based on 179,970 SNP loci from the whole genome of the tea plant, all of 142 cultivars were clearly divided into three groups: Assam type (CSA), Chinese type (CSS), and transitional type. Most CSA cultivars are from Yunnan Province, which confirms that Yunnan Province is the primary center of CSA origin and domestication. Most CSS cultivars are distributed in east China; therefore, we deduced that east China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. Moreover, 45 core markers were screened using strict criteria to 179,970 SNP loci, and we analyzed 117 well-Known tea cultivars in China with 45 core SNP markers. The results were as follows: (1) In total, 117 tea cultivars were distinguished by eight markers, which were selected to construct the DNA fingerprint, and the remaining markers were used as standby markers for germplasm identification. (2) Ten pairs of parent and offspring relationships were confirmed or identified, and among them, seven pairs were well-established pedigree relationships; the other three pairs were newly identified. In this study, the east of China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. The 45 core SNP markers were developed, which provide a scientific basis at the molecular level to identify the superior tea germplasm, undertake genetic relationship analysis, and benefit subsequent breeding work.
Interactive direct illumination in dynamic scenes using graphics APIS

Abstract We present a progressive refinement system for rendering direct illumination at interactive rates for dynamic scenes using available graphics APIs. We achieve the progression by subdividing object surfaces using a quad‐tree approach. Integrating the visibility and illumination, we can render scenes with soft shadows, taking into account the BRDFs of the scene objects. Our system allows a user to specify the desired frame rates, and the system will achieve such rates with the available time budget. Our system can also render dynamic scenes where the system restores the initial meshes and calculates illumination, producing finer but accurate soft shadows during iterative refinements.
Two‐layer organic photovoltaic cell

A thin‐film, two‐layer organic photovoltaiccell has been fabricated from copper phthalocyanine and a perylene tetracarboxylic derivative. A power conversion efficiency of about 1% has been achieved under simulated AM2 illumination. A novel feature of the device is that the charge‐generation efficiency is relatively independent of the bias voltage, resulting in cells with fill factor values as high as 0.65. The interface between the two organic materials, rather than the electrode/organic contacts, is crucial in determining the photovoltaicproperties of the cell.
Spin waves in multiple-spin-density-wave systems

The spin wave modes in an anisotropic Heisenberg model are investigated for a triple-spin-density-wave (TSDW) ground state in a FCC lattice. Explicit solutions are obtained in the diagonal-exchange regime in all directions. The solutions are also given in the (0,0, xi ) and ( xi , xi ,0) directions for the above model including non-diagonal exchange and a crystal-field term. Besides the usual acoustic spin wave modes the authors find a spin wave mode with a dispersion similar to that of a ferromagnetic spin wave. This latter mode couples weakly to neutrons. They obtain qualitatively different results to Jensen and Bak (1981) who appear to drop the off-diagonal-exchange terms. They also compare the results between a TSDW and those due to a distribution of single spin-density waves (SSDW) polarised along each of the axis directions and discuss their effect on width measurements.
Mechanism of PKCε regulation of cardiac GIRK channel gating

Significance Overactivity of a potassium ion channel (GIRK1/4) in the upper chambers of the heart has been thought to contribute to atrial fibrillation (AF), a widely prevalent heart rhythm abnormality or arrhythmia in the aging population and a significant cause of mortality. The treatment of AF is largely comprised of medications that correct heart rhythm, but are inadequate and have non-specific side effects. We have identified an amino acid on GIRK1/4, that when phosphorylated by the enzyme protein kinase C-ε, leads to increased GIRK1/4 activity. We explore the mechanism underlying channel overactivity in order to provide a strategy for drug discovery to reverse overactivity, without compromising the physiological function of the channel.
Toxin-like Peptides from the Bacterial Cultures Derived from Gut Microbiome Infected by SARS-CoV-2—New Data for a Possible Role in the Long COVID Pattern

It has been 3 years since the beginning of the SARS-CoV-2 outbreak, however it is as yet little known how to care for the acute COVID-19 and long COVID patients. COVID-19 clinical manifestations are of both pulmonary and extra-pulmonary types. Extra-pulmonary ones include extreme tiredness (fatigue), shortness of breath, muscle aches, hyposmia, dysgeusia, and other neurological manifestations. In other autoimmune diseases, such as Parkinson’s disease (PD) or Alzheimer’s Disease (AD), it is well known that role of acetylcholine is crucial in olfactory dysfunction. We have already observed the presence of toxin-like peptides in plasma, urine, and faecal samples from COVID-19 patients, which are very similar to molecules known to alter acetylcholine signaling. After observing the production of these peptides in bacterial cultures, we have performed additional proteomics analyses to better understand their behavior and reported the extended data from our latest in vitro experiment. It seems that the gut microbiome continues to produce toxin-like peptides also after the decrease of RNA SARS-CoV-2 viral load at molecular tests. These toxicological interactions between the gut/human microbiome bacteria and the virus suggest a new scenario in the study of the clinical symptoms in long COVID and also in acute COVID-19 patients. It is discussed that in the bacteriophage similar behavior, the presence of toxins produced by bacteria continuously after viral aggression can be blocked using an appropriate combination of certain drugs.
Exploring the Influence of Social Capital on HIV Prevention with Migrants from the Democratic Republic of Congo (DRC) Living in Durban, South Africa

Abstract Background: Research shows a growing attentiveness to the role of social and environmental influences on HIV risk behaviours. Moreover, the understanding of HIV risk behaviours has moved from an earlier consideration of individual risk, to ecological models, with the understanding that behaviours are rooted in the economic, environmental and social structure. Aim: To explore how social capital, specifically on a social bonding level, operates as a risk or protective factor for the spread of HIV among French-speaking migrants from the Democratic Republic of Congo (DRC), living in Durban, South Africa. Methods: A qualitative approach using a case study design was used to conduct the study. Data were collected through focus group discussions and individual in-depth interviews from a purposive sample of French-speaking migrants from DRC, living in Durban, South Africa. Ethical approval to conduct the study was obtained from the University of KwaZulu-Natal’s Human and Social Science Research Ethics’ Committee. Data were analysed thematically using Creswell’s steps of data analysis. Results: This study found that social capital can act as both a protective factor in certain circumstances, and a risk factor in others. Trust, norms, reciprocity and social networks are complex elements in the refugee community and are influenced by a myriad of factors including the past and present stressors that are prevalent within this community. Conclusions: The findings confirm the complexity of issues related to HIV prevention which necessitate policy and practice interventions to mitigate consequences that may result from the higher risks of HIV transmission in this community.
Tapered laser diode with linearly effective-refractive-index variation waveguide

We investigated a novel design concept of index-guided tapered LDs with linearly effective-refractive-index variation to make a quality beam in 808 nm for intermediate power LDs between a few decades of mW to ~ W. In this concept, the tapered width at each position in the propagation direction varies linearly depending on change in effective-refractive-index not geometry. We use GaAsP/InGaP/InGaAlP quantum well LD structure of 808 nm and standard LD fabrication processes to test. To design a detail structure, we use the effective-refractive-index method and transfer matrix method. The tapered ridge LD with linear effective-refractive-index variation shows more stable in beam quality but needs more study to optimize the structure.
Nation-State Threat Actor Attribution Using Fuzzy Hashing

Recent years have seen a rise in state-sponsored malware. Advanced Persistent Threat groups (APTs) have been waging a covert war with little repercussions due to the clandestine nature of cyberconflict. For sanctions to be imposed, malware attribution is an important stage in the attack analysis because the exploitation of known vulnerabilities via malware execution is one of the methods APT attackers use to establish a foothold in the target’s network. Prior attempts at automated attack attribution use behaviour report from sandboxes as inputs into machine learning algorithms. Whilst this is a good and reliable approach, it has some limitations. For example, some APT files may detect that they are in a sandboxed environment and stop execution or behave differently leading to false or no attributions. Hence, there is a need for an alternative feature extraction technique for attack attribution. This research proposes a novel framework for a lightweight and automated attack attribution that uses fuzzy hashes as natural language input for machine learning classifiers to attribute attacks. Experimental results show that the proposed framework attributes attack with average accuracy and F1-score of 89% and 87.5% for the country and APT group classification. In addition, we demonstrate how the proposed approach provides a faster and lightweight method of attack attribution, enhances advanced analysis of samples, and generates competitive performance with state-of-the-art dynamic analysis attribution engines.
Outdoor scene reflectance measurements using a Bragg-grating-based hyperspectral imager

The acquisition of spectral reflectance factor image data in an outdoor environment is a challenging task, mostly due to nonstatic scene content and illumination. In this work, we propose a work-flow for this task using a commercial Bragg-grating-based hyperspectral imager that can capture the visible and near-infrared part of the light spectrum. To our knowledge, we are the first who use this technology for outdoor spectral reflectance factor imaging. The work-flow involves focus position and exposure time estimation, illumination scaling, and image registration, among other procedures. Most of them generally apply to hyperspectral imaging, while some are specific to a Bragg-grating-based hyperspectral imaging device when dealing with specific challenges in outdoor environments. We have conducted some experiments to evaluate the quality of the acquired image data and discussed some limitations of the technology for spectral imaging of outdoor scenes. Fourteen urban scene spectral images acquired using the proposed approach are already publicly available to the scientific community under a Creative Commons license.