Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproducibility Problems of Amyloid-β Self-Assembly and How to Deal With Them

The self-assembly of peptides and proteins into amyloid fibrils and other aggregates are linked to several diseases. One of the most studied cases is the peptide amyloid-β (Aβ), found self-assembled in Alzheimer's disease patients' brains. In test tubes, assays with chemically synthesized or recombinant Aβ are widely investigated to understand the aggregation process and to find modulators, which could be of therapeutic interest. Experience over more than a decade in our laboratory through discussions with colleagues, expertly studying the literature, and as reviewers revealed to us the widely encountered difficulty to control the aggregation and obtain reproducible results in the test tube. However, this issue is scarcely reported and discussed in the publications, which we think hampers strongly the progress in this field and can deceive newcomers. Here, we describe the difficulty and potential reasons to obtain reproducible aggregation data and propose some guidelines for working with it.
Development and Validation of a Novel Risk Stratification Model for Cancer-Specific Survival in Diffuse Large B-Cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is a biologically and clinically heterogenous disease. Identifying more precise and individual survival prognostic models are still needed. This study aimed to develop a predictive nomogram and a web-based survival rate calculator that can dynamically predict the long-term cancer-specific survival (CSS) of DLBCL patients. A total of 3,573 eligible patients with DLBCL from 2004 to 2015 were extracted from the Surveillance, Epidemiology and End Results (SEER) database. The entire group was randomly divided into the training (n = 2,504) and validation (n = 1,069) cohorts. We identified six independent predictors for survival including age, sex, marital status, Ann Arbor stage, B symptom, and chemotherapy, which were used to construct the nomogram and the web-based survival rate calculator. The C-index of the nomogram was 0.709 (95% CI, 0.692–0.726) in the training cohort and 0.700 (95% CI, 0.671–0.729) in the validation cohort. The AUC values of the nomogram for predicting the 1-, 5-, and 10- year CSS rates ranged from 0.704 to 0.765 in both cohorts. All calibration curves revealed optimal consistency between predicted and actual survival. A risk stratification model generated based on the nomogram showed a favorable level of predictive accuracy compared with the IPI, R-IPI, and Ann Arbor stage in both cohorts according to the AUC values (training cohort: 0.715 vs 0.676, 0.652, and 0.648; validation cohort: 0.695 vs 0.692, 0.657, and 0.624) and K-M survival curves. In conclusion, we have established and validated a novel nomogram risk stratification model and a web-based survival rate calculator that can dynamically predict the long-term CSS in DLBCL, which revealed more discriminative and predictive accuracy than the IPI, R-IPI, and Ann Arbor stage in the rituximab era.
Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.
Dual-Mediation Paths Linking Corporate Social Responsibility to Employee’s Job Performance: A Multilevel Approach

This study attempts to examine the direct impact of corporate social responsibility (CSR) initiatives on employees’ job performance and the indirect relationships between CSR initiatives on employees’ job performance via industrial relations climate and psychological contract fulfillment. Data were collected from 764 supervisor–subordinate dyads and 271 middle managers from 85 companies. Using a multilevel approach, the results showed that organizational-level CSR was positively related to employees’ job performance. Moreover, the industrial relations climate and psychological contract fulfillment played mediating effects between CSR initiatives and job performance. This study provides novel theoretical evidence for why and how CSR initiatives improve job performance. Theoretical and practical implications for implementing CSR initiatives are discussed.
Extracellular Vesicles in Rheumatoid Arthritis and Systemic Lupus Erythematosus: Functions and Applications

In the last two decades, extracellular vesicles (EVs) have aroused wide interest among researchers in basic and clinical research. EVs, small membrane vesicles are released by almost all kinds of cells into the extracellular environment. According to many recent studies, EVs participate in immunomodulation and play an important role in the pathogenesis of autoimmune diseases. In addition, EVs have great potential in the diagnosis and therapy of autoimmune diseases. Here, we reviewed the latest research advances on the functions and mechanisms of EVs and their roles in the pathogenesis, diagnosis, and treatment of rheumatoid arthritis and systemic lupus erythematosus.
(−)-Epigallocatechin-3-Gallate Inhibits the Life Cycle of Pseudorabies Virus In Vitro and Protects Mice Against Fatal Infection

A newly emerged pseudorabies virus (PRV) variant with enhanced pathogenicity has been identiﬁed in many PRV-vaccinated swine in China since 2011. The PRV variant has caused great economic cost to the swine industry, and measures for the effective prevention and treatment of this PRV variant are still lacking. (–)-Epigallocatechin-3-gallate (EGCG) exhibits antiviral activity against diverse viruses and thus in this study, we investigated the anti-PRV activity of EGCG in vitro and in vivo. EGCG significantly inhibited infectivity of PRV Ra and PRV XJ5 strains in PK15 B6 cells and Vero cells. The anti-PRV activity of EGCG was dose-dependent, and 50 μM EGCG could completely block viral infection at different multiplicities of infection. We next revealed that EGCG blocked PRV adsorption and entry to PK15 B6 cells in a dose-dependent manner, but inhibition of PRV entry by EGCG was not as efficient as its inhibition of PRV adsorption. PRV replication was suppressed in PK15 B6 cells treated with EGCG post-infection. However, EGCG did not affect PRV assembly and could promote PRV release. Furthermore, 40 mg/kg EGCG provided 100% protection in BALB/c mice challenged with PRV XJ5, when EGCG was administrated both pre- and post-challenge. These results revealed that EGCG exhibits antiviral activity against PRV mainly by inhibiting virus adsorption, entry and replication in vitro. Meanwhile, EGCG increased the survival of mice challenged with PRV. Therefore, EGCG might be a potential antiviral agent against PRV infection.
Cell Proliferation and Collective Cell Migration During Zebrafish Lateral Line System Development Are Regulated by Ncam/Fgf-Receptor Interactions

The posterior lateral line system (pLLS) of aquatic animals comprises small clustered mechanosensory organs along the side of the animal. They develop from proneuromasts, which are deposited from a migratory primordium on its way to the tip of the tail. We here show, that the Neural Cell Adhesion Molecule Ncam1b is an integral part of the pathways initiating and regulating the development of the pLLS in zebrafish. We find that morpholino-knockdowns of ncam1b (i) reduce cell proliferation within the primordium, (ii) reduce the expression of Fgf target gene erm, (iii) severely affect proneuromast formation, and (iv) affect primordium migration. Ncam1b directly interacts with Fgf receptor Fgfr1a, and a knockdown of fgfr1a causes similar phenotypic changes as observed in ncam1b-morphants. We conclude that Ncam1b is involved in activating proliferation by triggering the expression of erm. In addition, we demonstrate that Ncam1b is required for the expression of chemokine receptor Cxcr7b, which is crucial for directed primordial migration. Finally, we show that the knockdown of ncam1b destabilizes proneuromasts, suggesting a further function of Ncam1b in strengthening the cohesion of proneuromast cells.
Internet of Things in Healthcare: Architecture, Applications, Challenges, and Solutions

Healthcare, the largest global industry, is undergoing signiﬁcant transformations with the genesis of a new technology known as the Internet of Things (IoT). Many healthcare leaders are investing more money for transforming their services to harness the beneﬁts provided by IoT, thereby paving the way for the Internet of Medical Things (IoMT), an extensive collection of medical sensors and associated infrastructure. IoMT has many beneﬁts like providing remote healthcare by monitoring health vitals of patients at a distant place, providing healthcare services to elderly people, and monitoring a large group of people in a region or country for detection and prevention of epidemics. This paper provides a review of IoT in the healthcare domain by ﬁrst describing the enabling technologies for delivering smart healthcare, followed by some of the key applications of IoT in healthcare. Next, a fog-based architecture consisting of three layers for IoT-based healthcare applications is proposed. Finally, we focus on some of the open challenges of IoT in healthcare, like fault tolerance, interoperability, latency, energy efﬁciency, and availability. Existing solutions for these challenges are also discussed.
Atypical Resting-State Functional Connectivity Dynamics Correlate With Early Cognitive Dysfunction in HIV Infection

Purpose: Previous studies have shown that HIV affects striato-cortical regions, leading to persisting cognitive impairment in 30–70% of the infected individuals despite combination antiretroviral therapy. This study aimed to investigate brain functional dynamics whose deficits might link to early cognitive decline or immunologic deterioration. Methods: We applied sliding windows and K-means clustering to fMRI data (HIV patients with asymptomatic neurocognitive impairment and controls) to construct dynamic resting-state functional connectivity (RSFC) maps and identify states of their reoccurrences. The average and variability of dynamic RSFC, and the dwelling time and state transitioning of each state were evaluated. Results: HIV patients demonstrated greater variability in RSFC between the left pallidum and regions of right pre-central and post-central gyri, and between the right supramarginal gyrus and regions of the right putamen and left pallidum. Greater variability was also found in the frontal RSFC of pars orbitalis of the left inferior frontal gyrus and right superior frontal gyrus (medial). While deficits in learning and memory recall of HIV patients related to greater striato-sensorimotor variability, deficits in attention and working memory were associated with greater frontal variability. Greater striato-parietal variability presented a strong link with immunologic function (CD4+/CD8+ ratio). Furthermore, HIV-infected patients exhibited longer time and reduced transitioning in states typified by weaker connectivity in specific networks. CD4+T-cell counts of the HIV-patients were related to reduced state transitioning. Conclusion: Our findings suggest that HIV alters brain functional connectivity dynamics, which may underlie early cognitive impairment. These findings provide novel insights into our understanding of HIV pathology, complementing the existing knowledge.
Localization in Wireless Sensor Networks for Accurate Event Detection

Event detection at its initial stage is considerably most demanding and more importantly challenging to reduce the causes and damages. The GPS-enabled sensor nodes are possibly a solution for the location estimation, but having GPS receiver in each sensor node makes the network costly. In this paper, the authors have presented a UNL, unknown node localization, method for the estimation of sensor location. The proposed method is based on RSSI, and there is no requirement of extra hardware and communication of data among the sensor nodes. The experiments are conducted in order to investigate the localization accuracy of UNL method, and they analyzed that the proposed method is simple as there is less computation and communication overhead. The proposed algorithm is further compared with other existing localization methods for the accurate estimation of unknown nodes. The experimental results show the effectiveness of the algorithm and its capability for locating the unknown nodes in a network more accurately.
An Improved Greener Esterification of Fatty Alcohols Using a Renewable Acid–Ionic Liquid Couple as Catalyst–Solvent

Abstract We have developed a simple and efficient method for the esterification of various organic acids with C4–C18 alcohols using the 1‐octyl‐3‐methylimidazolium tetrafluoroborate–para‐toluenesulphonic acid (OMIM/BF4–PTSA) couple, without organic solvent, either by classic heating or by microwave irradiation. The utilisation of the OMIM/BF4–PTSA couple presents considerable advantages: high yield, low temperature, short reaction time, isolation of the ester by simple decantation, easy reuse of the catalyst couple.
Mapping of colorectal carcinoma diseases with activation of Wnt/beta-catenin signalling pathway using hierarchical clustering approach

Aims To map the colorectal carcinoma (CRC) diseases with significant Wnt signalling pathway activation for delineating their clinicopathological and molecular profiles. Methods Mapping is based on hierarchical clustering analyses of a series of 283 CRCs. Data tabulated were histopathological patterns, immunophenotypic differentiation, RAS, RAF, CTNNB1 mutations and microsatellite instability status, tumour-infiltrating lymphocytes (TILs) and genetic setting. Beta-catenin expression in more than 10% of cell nuclei in the centre of tumour serves as a surrogate marker of significant activation of Wnt signalling pathway. Results Nuclei beta-catenin expression was present in 95% of CRCs; 56% of them met the criteria of high level of nuclei beta-catenin expression (≥10%). Proportion of beta-catenin positive nuclei was significantly higher in younger patients, rectal and left-sided colonic carcinomas. CRCs with high level of nuclei beta-catenin expression were regrouped into three clusters: (1) microsatellite stability (MSS) CRCs with no constitutive MAPK pathway activation including 90% of low-grade adenocarcinoma, NOS, with intestinal differentiation without TILs; (2) RAS-mutated MSS CRCs including low-grade adenocarcinoma, NOS, with intestinal differentiation and mucinous adenocarcinoma without TILs; (3) MSI-H CRCs including both BRAF-mutated CRCs evolving from serrated pathway and CTNNB1-mutated CRCs associated with Lynch syndrome. Conclusions MSS low-grade adenocarcinoma, NOS, with intestinal differentiation without TILs (‘crypt-like adenocarcinoma’) might be the morphological pending of canonical molecular subtype of CRC defined as displayed molecular epithelial differentiation and upregulation of WNT in consensus molecular classification of CRC.
Effects of a commercial mixture of herbal essential oils and vitamins (Provital®) and an organic acid (Totacid®) on performance and economical efficiency in broilers: A field study

A farm study was carried out to evaluate the inclusion of a commercially available blend of herbal essential oils (Provital) and an organic acid (Totacid) on productive performance and economical efficiency of broiler chickens. A total of 31,800 day old straight run broiler chickens (Ross 308) were allocated to three experimental treatments in three houses (10,600 birds per each) in a commercial farm for 50 days. Dietary treatments were a diet with no additive as control and diets containing 1 g/kg provital (A mixture of essential oils) or 1 g/kg Totacid. Birds fed on diets containing Provital and Totacid had numerically higher body weight than control and consumed lower feed. Inclusion of Provital and Totacid decreased feed conversion ratio noticeably and caused a noticeable reduction in mortality. Financial analysis showed that supplementation of diet with these additives increased return to investments and the returns were 18 and 10 times more than costs for Provital and Totacid, respectively. In conclusion, results of the present study showed that Provital and Totacid could be effective in enhancing broiler performance and the cost of adding them into the diet is very lower than the returns. Key words: Broiler, essential oil, organic acid, provital, totacid.
Structure of chemically deposited Zn(S,O,OH) buffer layer and the effects on the performance of Cu(in,Ga)Se2 solar cell

The effects of the immersion into a NH3 aqueous solution on the structural characteristics of the chemically deposited Zn(S,O,OH) layer and photovoltaic performance of the CIGS/Zn(S,O,OH) solar cells were investigated with structural and electrical characterizations. The as‐deposited‐Zn(S,O,OH) layer possessed a layered structure of upper Zn(OH)2 and Zn(S,O) layers, and the upper Zn(OH)2 layer was removed by the immersion. The conversion efficiency for the CIGS solar cell was improved from 6.8% to 13.7% by removing the upper Zn(OH)2 layer during the immersion. Copyright © 2015 John Wiley & Sons, Ltd.
Effects of Salinity and Water Stress on Growth and Macro Nutrients Concentration of Pomegranate (Punica granatum L.)

In order to study the effects of salinity and water stress on growth and macronutrients concentration of pomegranate plant leaves, a factorial experiment was conducted based on completely randomized design with 0, 30, and 60 mM of salinity levels of sodium chloride and calcium chloride (1:1) and three irrigation intervals (2, 4, and 6 days) with 3 replications on ‘Rabab’ and ‘Shishegap’ cultivars of pomegranate. The results of the shoot and root analysis indicated that the salinity and drought affected the concentration and distribution of sodium (Na+), potassium (K+), chloride (Cl−), calcium (Ca2+), magnesium (Mg2+), and phosphorus (P+) in pomegranate leaves. Mineral concentrations of sodium (Na+), chloride (Cl-), potassium (K+), in shoots and roots were increased with increasing salinity. Drought treatments increased the concentration of Cl−, Na+, and Mg2+ in the shoot. Both cultivars showed significant differences in the concentrations of elements, however the most accumulation of Na+ and Cl− was observed in ‘Rabab,’ while the ‘Shishegap’ cultivar had the most absorption of K+. ‘Shishegap’ cultivar showed higher tolerance to salinity than ‘Rabab’ through maintaining the vegetative growth and lower chloride transport to the shoot, and improvement of potassium transport to shoot.
Discounted-Sum Automata with Multiple Discount Factors

Discounting the influence of future events is a key paradigm in economics and it is widely used in computer-science models, such as games, Markov decision processes (MDPs), reinforcement learning, and automata. While a single game or MDP may allow for several different discount factors, discounted-sum automata (NDAs) were only studied with respect to a single discount factor. For every integer $\lambda\in\mathbb{N}\setminus\{0,1\}$, as opposed to every $\lambda\in \mathbb{Q}\setminus\mathbb{N}$, the class of NDAs with discount factor $\lambda$ ($\lambda$-NDAs) has good computational properties: it is closed under determinization and under the algebraic operations min, max, addition, and subtraction, and there are algorithms for its basic decision problems, such as automata equivalence and containment. We define and analyze discounted-sum automata in which each transition can have a different integral discount factor (integral NMDAs). We show that integral NMDAs with an arbitrary choice of discount factors are not closed under determinization and under algebraic operations and that their containment problem is undecidable. We then define and analyze a restricted class of integral NMDAs, which we call tidy NMDAs, in which the choice of discount factors depends on the prefix of the word read so far. Some of their special cases are NMDAs that correlate discount factors to actions (alphabet letters) or to the elapsed time. We show that for every function $\theta$ that defines the choice of discount factors, the class of $\theta$-NMDAs enjoys all of the above good properties of integral NDAs, as well as the same complexity of the required decision problems. Tidy NMDAs are also as expressive as deterministic integral NMDAs with an arbitrary choice of discount factors. All of our results hold for both automata on finite words and automata on infinite words.
The response of soil quality indicators to conservation management

The response of soil quality attributes to management practices across a diverse range of farming systems is key to identifying a robust minimum data set (MDS). The objectives of this study were to compare the response and consistency of different soil organic matter (SOM) attributes to changes in soil management practices in eastern Canadian agroecosystems. Soil samples (0–10 cm) were obtained at sites of several replicated experiments throughout eastern Canada, and 16 paired comparisons were selected to determine the effect of conservation (no-tillage, rotations, organic amendments) versus conventional (fall moldboard plowing, continuous cropping, no organic amendments) management practices. A sensitivity index was calculated for each of the attributes by dividing the values for conservation treatments with their conventionally managed counterparts (i.e., Conservation/Conventional). The index showed that light fraction (LF) N (1.58) and macro-organic matter-N (MOM-N) (1.54) were the most sensitive SOM a.
The use of sewage sludge as an organic matter source in apple trees.

The objective of this experiment was to evaluate the effects of different doses of sludge on fruit yield, growth, nutrition and heavy metal accumulation of apple trees on a calcareous soil 1999-2003. Sewage sludge was added to the soil at rates of 0, 10, 20, 40 and 60 kg tree -1 . Manure was applied to the soil at a rate of 25 kg tree -1 . According to four-years data, cumulative application of sewage sludge to apple trees significantly increased fruit yield, trunk cross-sectional area, shoot growth and leaf N, Mg, Fe, Mn, Zn and Cu contents at the end of the study. Leaf Ni slightly increased with sludge addition in 2003 only. The four-year results of this study indicated that repeated sewage sludge application to apple trees did not cause toxicity in leaves and fruits. However, long-term sewage sludge application may result in the accumulation of Zn, Cu and Ni in the soil and plant.