Miracle-dz/UniFAR-FTUs huggingface dataset:
β‐Strand‐mediated interactions of protein domains

Protein domains exist by themselves or in combination with other domains to form complex multidomain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β‐sheet is known to be particularly troublesome for automatic structure‐based domain decomposition pipelines. Here, we study edge‐to‐edge β‐strand interactions between domains in a protein chain, to help define the boundaries for some more difficult cases where a single β‐sheet spanning over two domains gives an appearance of one. We give a number of examples where β‐strands belonging to a single β‐sheet do not belong to a single domain and highlight the difficulties of automatic domain parsers on these examples. This work can be used as a baseline for defining domain boundaries in homologous proteins or proteins with similar domain interactions in the future.
Does Perceived Ageism Widen the Digital Divide? And Does It Vary by Gender?

BACKGROUND AND OBJECTIVES Existing literature presents a widening digital divide among older adults in addition to the consideration of the potential adverse impacts of ageism on internet use among the older adult population. Our study aimed to investigate (1) whether older adults' perceived ageism will be associated with their use of the internet and (2) whether the relationship between perceived ageism and internet use will be moderated by age groups and binary gender. RESEARCH DESIGN AND METHOD Using the data from the 2016 Health and Retirement Study, regression analyses were separately performed by gender. Two measures of perceived ageism were considered: (1) self-perception of aging and (2) perceived age discrimination. RESULTS Our findings suggested that greater exposure to ageism is generally related to less use of the internet. In addition, we found divergent patterns in the relationship between ageism and internet use by gender. For women, a lower level of internet use was predicted by more negative perceptions of aging, whereas men's internet use was associated with the experience of age discrimination. Furthermore, interaction effects between age groups and ageism varied across gender. The negative perception of aging was more strongly associated with less internet use in older women than middle-aged women. In comparison, the perceived age discrimination predicted less internet use in middle-aged men than older men. DISCUSSION AND IMPLICATIONS Our findings suggest that perceived ageism is significantly associated with internet use, and its association differs by gender.
ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)

Abstract Meadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. It is a diploid (2n = 14) outbreeding species that belongs to the genus Festuca. Together with Lolium perenne, they are the most important genera of forage grasses. Meadow fescue has very high quality of yield with good winter survival and persistency. However, extensive genomic resources for meadow fescue have not become available so far. To address this lack of comprehensive publicly available datasets, we have developed functionally annotated draft genome sequences of two meadow fescue genotypes, ‘HF7/2’ and ‘B14/16’, and constructed the platform ForageGrassBase, available at http://foragegrass.org/, for data visualization, download and querying. This is the first open-access platform that provides extensive genomic resources related to this forage grass species. The current database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes that can be accessed using Genome Browser (GBrowse), along with comparative genomic alignments to Arabidopsis, L. perenne, barley, rice, Brachypodium and maize genomes. We have integrated homologous search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadable data gives a user-friendly access to meadow fescue genomic resources. To our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. The current forage grass database provides valuable resources for a range of research fields related to meadow fescue and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org.
(MIS)Use of the Adverse Outcome Pathway Concept for Assessing Endocrine Disruption in Nontarget Organisms

Integr Environ Assess Manag 2020:525–530 Debates, Dilemmas, and Discoveries (3D) offers rapid publication on compelling and timely issues. Contributions should answer the “so what? ” question and should encourage readers to think, challenge them to do better science, and motivate them to excel in the ways in which they apply science to environmental assessment and management. The new feature will provide a platform to: report on progress in fi eld and laboratory research explore new or emerging research questions provide opinions and perspectives on a range of environmental topics debate issues spotlight management policies and practices share challenges and insights on biology, chemistry, ecology, engineering and sustainability Guidelines and Submission: Manuscripts should be concise and written for a broad audience of policy makers, scientists, and business professionals. Manuscripts are limited to 1000 words and may include no more than 1 table or fi gure and up to 6 references. Manuscripts are subject to review and approval by the 3D Editors. Submit any questions and manuscripts directly to the 3D Editors (ieam3d@setac.org). In a Nutshell. Debates, Dilemmas, and Discoveries 525
Nontypeable Haemophilus influenzae Type IV Pilus Mediates Augmented Adherence to Rhinovirus-Infected Human Airway Epithelial Cells

Human rhinovirus (hRV) is frequently detected in the upper respiratory tract, and symptomatic infection is associated with an increased nasopharyngeal bacterial load, with subsequent development of secondary bacterial diseases. Nontypeable Haemophilus influenzae (NTHI) is a commensal bacterial species of the human nasopharynx; however, in the context of prior or concurrent upper respiratory tract viral infection, this bacterium commonly causes multiple diseases throughout the upper and lower respiratory tracts. ABSTRACT Human rhinovirus (hRV) is frequently detected in the upper respiratory tract, and symptomatic infection is associated with an increased nasopharyngeal bacterial load, with subsequent development of secondary bacterial diseases. Nontypeable Haemophilus influenzae (NTHI) is a commensal bacterial species of the human nasopharynx; however, in the context of prior or concurrent upper respiratory tract viral infection, this bacterium commonly causes multiple diseases throughout the upper and lower respiratory tracts. The present study was conducted to determine the mechanism(s) by which hRV infection promotes the development of NTHI-induced diseases. We showed that hRV infection of polarized primary human airway epithelial cells resulted in increased adherence of NTHI, due in part to augmented expression of CEACAM1 and ICAM1, host cell receptors to which NTHI binds via engagement of multiple adhesins. Antibody blockade of these host cell receptors significantly reduced NTHI adherence. With a specific focus on the NTHI type IV pilus (T4P), which we have previously shown binds to ICAM1, an essential adhesin and virulence determinant, we next showed that T4P-directed antibody blockade significantly reduced NTHI adherence to hRV-infected airway cells and, further, that expression of this adhesin was required for the enhanced adherence observed. Collectively, these data provide a mechanism by which “the common cold” promotes diseases due to NTHI, and they add further support for the use of PilA (the majority subunit of T4P) as a vaccine antigen, since antibodies directed against PilA are expected to limit the notably increased bacterial load associated with hRV coinfection and thereby to prevent secondary NTHI-induced diseases of the respiratory tract.
Gene expression and prognosis of sirtuin family members in ovarian cancer

Abstract Sirtuins (SIRTs), a class of nicotinamide-adenine dinucleotide (NAD)+-dependent deacetylases, involve in modulating carcinogenesis and progression of various malignancies through their regulation of the cancer metabolism. However, the expression profiles and prognostic roles of SIRTs in ovarian cancer (OC) remain unclear. We underscore the transcriptional expression and prognostic significance of SIRTs in OC patients using online databases. Gene Expression Profiling Interactive analysis (GEPIA) was applied to analyze mRNA expression, and Kaplan–Meier plotter was used to evaluate prognostic value. In patients with OC, SIRT1/2/3 were significantly down-regulated, while rest of SIRTs were not significantly changed. High SIRT2/5/6/7 expression was correlated with favorable overall survival (OS), while high SIRT1/4 expression was correlated with poor OS. Additionally, aberrant SIRTs mRNA levels were related to the prognosis of OC patients with different clinicopathological characteristics. This is the first study to integrate bioinformatics approaches intended to identify the expression profiles and prognostic value of SIRTs in OC. These results suggest that SIRTs is related to the prognosis of OC and may be the potential therapeutic interventions in OC.
Correlation Designs and Analyses

The clinical nurse specialist is frequently the person within the nursing department who leads nursing research studies. Because there are so many options available and these options are predicated on the research questions (Table 1) and the level of measurement, it is important that the clinical nurse specialist is aware of the options and criteria used to make the best option selections. Research designs are typically designated as qualitative or quantitative. The 4 major quantitative designs are classified as descriptive, correlation, quasi-experimental, and experimental. The purpose of this article is to provide important information needed to design, conduct, and analyze a correlation study.
Features of Childhood Maltreatment and Resilience Capacity in Adulthood: Results from a Large, Community-Based Sample.

Childhood maltreatment is consistently associated with poor outcomes. However, few epidemiological studies have examined the association between childhood maltreatment and adult resilience capacity, defined as one's perceived ability to cope successfully with challenges. This study aimed to determine associations between adult resilience capacity and specific types and features of childhood maltreatment. Participants were African American adults recruited from a public urban hospital in Atlanta, GA (N = 1,962) between 2005 and 2013. Childhood maltreatment, including witnessing domestic violence or physical, emotional, and sexual abuse, was assessed retrospectively using the Traumatic Events Inventory. Perceived resilience capacity was assessed using the Connor-Davidson Resilience Scale. Linear regressions were performed assessing the association between resilience capacity and childhood maltreatment exposure in general, as well as specific dimensions of exposure, including type, co-occurrence, and developmental timing, adjusting for covariates. Participants exposed to any maltreatment reported lower resilience capacity than unexposed peers, B = -0.38, SE = 0.04, p < . 001. All maltreatment types were negatively associated with resilience capacity, even after adjusting for other lifetime trauma exposure. Only emotional abuse remained significantly associated with resilience capacity after accounting for current psychological distress, B = -0.11, SE = 0.05, p = . 022. Maltreatment co-occurrence followed an inverse dose-response relationship with resilience capacity: For each additional maltreatment type, scores decreased by 0.18 units (SD = 0.02), p < . 001. Finally, the developmental timing of maltreatment did not reveal any differential influences on resilience capacity. The results suggest that childhood emotional abuse and co-occurrence of maltreatment types may be particularly deleterious to adult resilience capacity.
Cross-cultural adaptation, reliability, and validation of the Taiwan-Chinese version of Cumberland Ankle Instability Tool

Abstract Purpose To cross-cultural translate the Cumberland Ankle Instability Tool (CAIT) to Taiwan-Chinese version (CAIT-TW), and to evaluate the validity, reliability and cutoff score of CAIT-TW for Taiwan-Chinese athletic population. Materials and methods The English version of CAIT was translated to CAIT-TW based on a guideline of cross-cultural adaptation. 77 and 58 Taiwanese collegial athletes with and without chronic ankle instability filled out CAIT-TW, Taiwan-Chinese version of Lower Extremity Functional Score (LEFS-TW) and Numeric Rating Scale (NRS). The construct validity, test-retest reliability, internal consistency and cutoff score of CAIT-TW were evaluated. Results In construct validity, the Spearman’s correlation coefficients were moderate (CAIT-TW vs LEFS-TW: Rho = 0.39, p < 0.001) and strong (CAIT-TW vs NRS: Rho= 0.76, p < 0.001). The test retest reliability was excellent (ICC2.1 = 0.91, 95% confidential interval = 0.87–0.94, p < 0.001) with a good internal consistency (Cronbach’s α: 0.87). Receiver operating characteristic curve showed a cutoff score of 21.5 (Youden index: 0.73, sensitivity: 0.87, specificity 0.85). Conclusions The CAIT-TW is a valid and reliable tool to differentiate between stable and instable ankles in athletes and may further apply for research or daily practice in Taiwan. Implications for rehabilitation For athletes, chronic ankle instability is prevalent and causes negative sequela, such as lowered quality of daily life, affected functional performance, and may cause post traumatic osteoarthritis. The psychometric properties of the Taiwan-Chinese version of the Cumberland Ankle Instability Tool showed moderate to strong construct validity, excellent test retest reliability, a good internal consistency and a cutoff score of 21.5. The validity and reliability of the Taiwan-Chinese version of the Cumberland Ankle Instability Tool are to enable clinicians to evaluate and manage ankle instability in Taiwanese who speaks Mandarin Chinese.
Detection of rabies virus antigen by the indirect rapid immunohistochemistry test in equines and comparisons with other diagnostic techniques

Laboratory diagnosis of rabies in equines is essential for distinguishing the disease from other sources of encephalitis. Diagnosis by conventional techniques such as a direct fluorescent antibody test (dFAT) or viral isolation in mice or cell culture can be difficult, and the application of molecular biological methods may be necessary. We performed an indirect rapid immunohistochemistry test (iRIT) for the detection of the rabies virus (RABV) antigen in the central nervous system (CNS) of equines and compared the results with those of other diagnostic techniques. We reviewed result records from the Rabies Diagnosis Laboratory at Instituto Pasteur, São Paulo, Brazil, of 174 samples of equine CNS from July 2014 to June 2016, which were investigated by dFAT, rabies tissue culture infection test (RTCIT), mouse inoculation test (MIT) and reverse transcription‐polymerase chain reaction (RT‐PCR) followed by genetic sequencing. These samples, 29 presented divergent results among techniques and were selected for the performed in the iRIT. The detected positivity rate was 4/29 (14%) by dFAT, 5/28 (18%) by RTCIT, 10/29 (35%) by MIT and 26/27 (96%) by RT‐PCR. We analysed 29 samples through imprints of the cortex, hippocampus, cerebellum and brainstem in slides fixed in 10% buffered formaldehyde. Eighteen samples were identified as positive (62%) by iRIT assay, representing a greater number of positive cases than that detected by dFAT, MIT and RTCIT but not by RT‐PCR. Among the brain regions, the brainstem presented the highest positivity (78%), followed by the hippocampus (69%), cerebellum (67%) and cortex (67%). Our results provide evidence that iRIT can contribute to a rapid diagnosis of rabies in equines and that complementary tests should be used to improve diagnostic accuracy in this species.
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks

Intrinsically disordered regions (IDR) play an important role in key biological processes and are closely related to human diseases. IDRs have great potential to serve as targets for drug discovery, most notably in disordered binding regions. Accurate prediction of IDRs is challenging because their genome wide occurrence and a low ratio of disordered residues make them difficult targets for traditional classification techniques. Existing computational methods mostly rely on sequence profiles to improve accuracy which is time consuming and computationally expensive. This article describes an ab initio sequence‐only prediction method—which tries to overcome the challenge of accurate prediction posed by IDRs—based on reduced amino acid alphabets and convolutional neural networks (CNNs). We experiment with six different 3‐letter reduced alphabets. We argue that the dimensional reduction in the input alphabet facilitates the detection of complex patterns within the sequence by the convolutional step. Experimental results show that our proposed IDR predictor performs at the same level or outperforms other state‐of‐the‐art methods in the same class, achieving accuracy levels of 0.76 and AUC of 0.85 on the publicly available Critical Assessment of protein Structure Prediction dataset (CASP10). Therefore, our method is suitable for proteome‐wide disorder prediction yielding similar or better accuracy than existing approaches at a faster speed.
Inflammation, oxidative stress and genotoxicity responses to biodiesel emissions in cultured mammalian cells and animals

Abstract Biodiesel fuels are alternatives to petrodiesel, especially in the transport sector where they have lower carbon footprint. Notwithstanding the environmental benefit, biodiesel fuels may have other toxicological properties than petrodiesel. Particulate matter (PM) from petrodiesel causes cancer in the lung as a consequence of delivery of genotoxic polycyclic aromatic hydrocarbons, oxidative stress and inflammation. We have reviewed articles from 2002 to 2019 (50% of the articles since 2015) that have described toxicological effects in terms of genotoxicity, oxidative stress and inflammation of biodiesel exhaust exposure in humans, animals and cell cultures. The studies have assessed first generation biodiesel from different feedstock (e.g. rapeseed and soy), certain second generation fuels (e.g. waste oil), and hydrogenated vegetable oil. It is not possible to rank the potency of toxicological effects of specific biodiesel fuels. However, exposure to biodiesel exhaust causes oxidative stress, inflammation and genotoxicity in cell cultures. Three studies in animals have not indicated genotoxicity in lung tissue. The database on oxidative stress and inflammation in animal studies is larger (13 studies); ten studies have reported increased levels of oxidative stress biomarkers or inflammation, although the effects have been modest in most studies. The cell culture and animal studies have not consistently shown a different potency in effect between biodiesel and petrodiesel exhausts. Both increased and decreased potency have been reported, which might be due to differences in feedstock or combustion conditions. In conclusion, combustion products from biodiesel and petrodiesel fuel may evoke similar toxicological effects on genotoxicity, oxidative stress and inflammation.
Unraveling and Mapping the Mechanisms for Near-surface Microstructure Evolution in CuNi Alloys under Sliding.

The origin of friction and wear in polycrystalline materials is intimately connected with their microstructural response to interfacial stresses. Although many mechanisms that govern microstructure evolution in sliding contacts are generally understood, it is still a challenge to ascertain which mechanisms matter under what conditions, which limits the development of tailor-made microstructures for reducing friction and wear. Here, we shed light on the circumstances that promote plastic deformation and surface damage by studying several FCC CuNi alloys subjected to sliding with molecular dynamics simulations featuring tens of millions of atoms. By analyzing the depth- and time-dependent evolution of the grain size, twinning, shear, and the stresses in the aggregate, we derive a deformation mechanism map for CuNi alloys. We verify the predictions of this map against focused ion beam images of the near-surface regions of CuNi alloys that were experimentally subjected to similar loading conditions. Our results may serve as a tool for finding optimum material compositions within a specified operating range.
First steps towards sustainability? University freshmen perceptions on nature versus environment

The Global Earth Overshoot Day, the date when all annually available natural resources are consumed, is set for July this year. For densely populated European countries like Germany or Switzerland, that specific day is due even earlier (May). To overcome such an unsustainable lifestyle, immediate actions are required, which includes substantial educational efforts. As the model of "Sustainable Development" is complex, appropriate pedagogical actions need to support cognitive learning, critical thinking and behavioural actions. Knowledge about individual conceptions in relation to the Environment, Nature and Ecological Footprints contributes to pre-conditions to succeed. To what extent present teaching methods influenced individual conceptions during the first UN-decade regarding those terms is illustrated by 464 Swiss-German university freshmen who participated in our paper-pencil test, which is based on four open questions. The term of Environment was perceived as the sum of biocentric, ecocentric and anthropocentric views. The participants often equated the term to Nature and associated it with positive feelings or emotions. Therefore, calm, joy and aesthetic appreciation were predominantly named. Regardless of the concept, humans were perceived as the Greatest Environmental Threat. In contrast, recommendations to reduce Environmental Footprints regarding mobility & transport, waste avoidance and consumption differ. Following a binary logistic regression analysis, the involvement of the Inclusion of Self Scale (INS) was used as an explanatory variable to detect patterns of those conceptions. Relating sustainable concepts, natural resources were frequently named exceeding saving water and energy or other association dealt with second-hand issues or regional/ seasonal usages. Such ideas are shaped by experiences and scientific expertise.