Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Linkage Peaks Discovered for Diabetic Nephropathy in Individuals With Type 1 Diabetes

Genome-wide association studies (GWAS) and linkage studies have had limited success in identifying genome-wide significantly linked regions or risk loci for diabetic nephropathy (DN) in individuals with type 1 diabetes (T1D). As GWAS cohorts have grown, they have also included more documented and undocumented familial relationships. Here we computationally inferred and manually curated pedigrees in a study cohort of >6,000 individuals with T1D and their relatives without diabetes. We performed a linkage study for 177 pedigrees consisting of 452 individuals with T1D and their relatives using a genome-wide genotyping array with >300,000 single nucleotide polymorphisms and PSEUDOMARKER software. Analysis resulted in genome-wide significant linkage peaks on eight chromosomal regions from five chromosomes (logarithm of odds score >3.3). The highest peak was localized at the HLA region on chromosome 6p, but whether the peak originated from T1D or DN remained ambiguous. Of other significant peaks, the chromosome 4p22 region was localized on top of ARHGAP24, a gene associated with focal segmental glomerulosclerosis, suggesting this gene may play a role in DN as well. Furthermore, rare variants have been associated with DN and chronic kidney disease near the 4q25 peak, localized on top of CCSER1.
Quantifying people’s experience during flood events with implications for hazard risk communication

Semantic drift is a well-known concept in distributional semantics, which is used to demonstrate gradual, long-term changes in meanings and sentiments of words and is largely detectable by studying the composition of large corpora. In our previous work, which used ontological relationships between words and phrases, we established that certain kinds of semantic micro-changes can be found in social media emerging around natural hazard events, such as floods. Our previous results confirmed that semantic drift in social media can be used to for early detection of floods and to increase the volume of ‘useful’ geo-referenced data for event monitoring. In this work we use deep learning in order to determine whether images associated with ‘semantically drifted’ social media tags reflect changes in crowd navigation strategies during floods. Our results show that alternative tags can be used to differentiate naïve and experienced crowds witnessing flooding of various degrees of severity.
Molecular characterization of recent HoBi-like pestivirus (HoBiPeV) isolates from cattle showing mucosal disease-like signs in India reveals emergence of a novel genetic lineage.

Natural infections with HoBi-like pestivirus (HoBiPeV) have been detected in cattle in South America, Europe and Asia with a range of clinical manifestations including fatal mucosal disease (MD). In India, although HoBiPeV in cattle has been reported, there is no information on currently circulating HoBiPeV strains and associated severe clinical disease. Between September 2018 and December 2019, suspected cases of bovine viral diarrhea with severe disease in cattle were noticed in farmers' small holdings in Tamil Nadu State. To determine the extent of pestivirus infection, blood, serum, nasal or oral swab samples of 46 cattle from 18 villages were tested. Based on the real-time RT-PCR, antigen ELISA and nucleotide sequencing results, pestivirus was detected in nine cattle from eight villages in two districts and all pestiviruses were identified as HoBiPeV. All nine HoBiPeV infected cattle displayed clinical signs resembling MD and HoBiPeV isolates (n=9) obtained were characterized at genetic and antigenic level. Phylogenetic analyses based on 5'-UTR, Npro and combined 5'-UTR-Npro gene sequences revealed that eight HoBiPeV isolates clustered into a clade, distinct from all reported HoBiPeV clades (a-d), whereas one belonged to HoBiPeV-d clade, thus providing evidence of emergence of a novel HoBiPeV clade (e). This was also supported by HoBiPeV-e clade specific amino acid substitutions in Npro and the antigenic reactivity patterns. The study demonstrates the existence and independent evolution of five HoBiPeV clades (four main clades) globally and surprisingly three exclusive to India. Also we confirm first HoBiPeV occurrence in southern India with predominant prevalence of HoBiPeV-e strains. Besides demonstrating increased HoBiPeV genetic diversity, here we show association of HoBiPeV with severe clinical disease involving fatalities highlighting impact of HoBiPeV on cattle health. The emergence of a novel HoBiPeV lineage provides new insights on global HoBiPeV epidemiology and genetic diversity reiterating the need for continuous monitoring of HoBiPeV in India.
Maintaining Sense of Purpose Following Health Adversity in Older Adulthood: A Propensity Score Matching Examination.

OBJECTIVES Research has demonstrated sense of purpose predicts better health in older adulthood. However, work is limited with respect to understanding how experiencing a health event or illness diagnosis impacts older adults' sense of purpose. METHOD The current study employed a propensity score matching approach to compare older adults who did or did not experience an adverse health event on changes in sense of purpose across three waves of the Health and Retirement Study. Sense of purpose was assessed at each wave, and changes were compared between people who did versus did not experience one of seven diagnoses and health events. RESULTS When propensity score matching was employed, no differences in trajectories of change for sense of purpose were found with respect to all seven events. Individual differences in trajectories though were evidenced across groups. DISCUSSION The current findings suggest that even when health events impact older adults' physical functioning or place limitations on their activity, it may hold little ramifications for their sense of purpose. Future research should consider this potential for resilience, focusing on how adults compensate for losses.
Retrospective prediction of the epidemic trend of COVID‐19 in Wuhan at four phases

The coronavirus disease 2019 (COVID‐19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) began in December 2019 and was basically under control in April 2020 in Wuhan. To explore the impact of intervention measures on the COVID‐19 epidemic, we established susceptible–exposed–infectious–recovered (SEIR) models to predict the epidemic characteristics of COVID‐19 at four different phases (beginning, outbreak, recession, and plateau) from January 1st to March 30th, 2020. We found that the infection rate rapidly grew up to 0.3647 at Phase II from 0.1100 at Phase I and went down to 0.0600 and 0.0006 at Phase III and IV, respectively. The reproduction numbers of COVID‐19 were 10.7843, 13.8144, 1.4815, and 0.0137 at Phase I, II, III, and IV, respectively. These results suggest that intensive interventions, including compulsory home isolation and rapid improvement of medical resources, can effectively reduce the COVID‐19 transmission. Furthermore, the predicted COVID‐19 epidemic trend by our models was close to the actual epidemic trend in Wuhan. Our phase‐based SEIR models demonstrate that intensive intervention measures can effectively control COVID‐19 spread even without specific medicines and vaccines against this disease.
A complex systems perspective of news recommender systems: Guiding emergent outcomes with feedback models

Algorithms are increasingly making decisions regarding what news articles should be shown to online users. In recent times, unhealthy outcomes from these systems have been highlighted including their vulnerability to amplifying small differences and offering less choice to readers. In this paper we present and study a new class of feedback models that exhibit a variety of self-organizing behaviors. In addition to showing important emergent properties, our model generalizes the popular “top-N news recommender systems” in a manner that provides media managers a mechanism to guide the emergent outcomes to mitigate potentially unhealthy outcomes driven by the self-organizing dynamics. We use complex adaptive systems framework to model the popularity evolution of news articles. In particular, we use agent-based simulation to model a reader’s behavior at the microscopic level and study the impact of various simulation hyperparameters on overall emergent phenomena. This simulation exercise enables us to show how the feedback model can be used as an alternative recommender to conventional top-N systems. Finally, we present a design framework for multi-objective evolutionary optimization that enables recommendation systems to co-evolve with the changing online news readership landscape.
A Participatory Group Process within a Health Collaborative to Collect and Disseminate Needs Assessment Data

Abstract:Background: Inclusion of community-based participatory research (CBPR) principles within an epidemiological study design is anticipated to promote the effective integration of knowledge derived from research data collection into the strategic planning and collaborative effort of a group focused on improving community-based health outcomes. This article describes how CBPR principles were used throughout survey design, data collection, analyses and results dissemination.Methods: A health needs assessment survey was developed as a partnership between an academic research group from the Virginia Commonwealth University (VCU), a neighborhood-level health and wellness collaborative, and community residents. Survey development, pilot testing, data collection, results dissemination, and action among the health collaborative members were carried out using CBPR principles. Feedback from participants at each stage was collected to improve the overall process of data use within the collaborative.Results: Data from 1,064 adult participants living in the East End of Richmond, Virginia, were collected. The use of CBPR and epidemiological approaches was successful in promoting effective collaborative efforts, as indicated by 1) sustained organization-level partner participation in the development of survey items and donation of participant incentives; 2) positive feedback from resident- and organization-level participants in a preliminary data dissemination event; 3) strong resident participation at community-wide dissemination events; 4) increases in survey-related blog traffic occurring in conjunction with community-wide dissemination events; and 5) the use of process protocols and results within similar collaboratives across the city.Conclusions: Use of CBPR principles with epidemiological methods is a powerful tool for facilitating effective community-level strategic planning within health collaboratives.
Prevalence of current and former smoking in industrial workers worldwide: a systematic review and meta-analysis

Abstract Objectives One of the health problems in recent decades is the prevalence of smoking in the world. In this study, the global prevalence of smoking in industrial workers was investigated using meta-analysis. Method The method of the present study was a systematic review and meta-analysis. Three scientific sources, PubMed, Web of Science, and Scopus, were selected for the search, and these databases were searched until September 2020. Random effects method was used for the analysis and then the analysis was performed for the type of smoking (Current, Former), gender, and continent. Heterogeneity was examined in all analyses. Result A total of 88 studies were included in the meta-analysis. The prevalence of smoking in industrial workers was 41% also the confidence interval was 35–48%. The prevalence of current smoking in industrial workers was 39% also the confidence interval was 29–48%. The prevalence of former smoking in industrial workers was 18% also the confidence interval was 13–22%. I 2 heterogeneity test was 99.9%. Discussion From the findings of the present study, it can be seen that industrial workers are more exposed to smoking compared to the general population, and this can put their health at greater risk.
Kinetics and mechanism of chromic acid oxidation of chalcones (phenyl styryl ketones)

The kinetics of the oxidation by chromic acid of chalcone (phenyl styryl ketone) and several substituted chalcones have been investigated in 95%(v/v) acetic acid. The reaction is overall of the second order, first order in each reactant. The parameters of Arrhenius and transition state theories have been computed. The enthalpies of activation are in the range 12·3–19·4 kcal mol–1 and the entropies of activation range from –5 to –22 cal mol–1 K–1. The effect of substituents on the rate of oxidation has been evaluated. A Hammett-type correlation with Brown's σ+ values has been established with ρ+–1·2. The data are consistent with a mechanism which involves electrophilic attack of chromic acid at the carbon–carbon double bond resulting in the formation of an epoxide.
Identification of flavonoid 8-hydroxylase with gossypetin synthase activity from flower specific EST data of Lotus Japonicus.

Lotus japonicus is a model legume, that accumulates 8-hydroxyflavonol derivatives such as gossypetin (8-hydroxyquercetin) 3-O-glycoside, which confer the yellow color to its petals. An enzyme, flavonoid 8-hydroxylase (LjF8H), is assumed to be involved in the biosynthesis, but the specific gene is yet to be identified. The LjF8H cDNA was isolated as an FAD-binding monooxygenase-like protein using flower buds and flower specific EST data of L. japonicus. LjF8H is a single copy gene on chromosome III consisting of six exons. The conserved FAD- and NAD(P)H-dependent oxidase motifs were found in LjF8H. Phylogenetic analysis suggested that LjF8H is a member of the flavin monooxygenase group, but distinctly different from other known flavonoid oxygenases. Analysis of recombinant yeast microsome expressing LjF8H revealed that the enzyme catalyzed the 8-hydroxylation of quercetin. Other flavonoids, such as naringenin, eriodictyol, apigenin, luteolin, taxifolin, and kaempferol also acted as substrates of LjF8H. This broad substrate acceptance was unlike known F8Hs in other plants. Interestingly, flavanone and flavanonol, which have saturated C-C bond at positions 2 and 3 of the flavonoid C-ring, produced 6-hyroxylflavonoids as a by-product of the enzymatic reaction. Furthermore, LjF8H only accepted the 2S-isomer of naringenin, suggesting the conformational state of the substrates might affect product specificity. The overexpression of LjF8H in Arabidopsis thaliana and Petunia hybrida synthesized gossypetin and 8-hydroxykaempferol, respectively, indicating that LjF8H was functional in plant cells. In conclusion, this study represents the first instance of cloning and identification of F8Hs responsible for gossypetin biosynthesis.
A small angle x-ray scattering study of the droplet–cylinder transition in oil-rich sodium bis(2-ethylhexyl) sulfosuccinate microemulsions

A method for nonlinear fitting of x-ray scattering data from polydisperse mixtures was developed. It was applied to the analysis of the structural changes in the droplet phase of oil-rich water-in-oil (w/o) sodium bis(2-ethylhexyl) sulfosuccinate (AOT) microemulsions with increasing temperature or upon addition of salt. Data were collected at different temperatures (15 to 60 °C) and salt concentrations (up to 0.6% NaCl) within the one-phase region of the L2 phase (w/o microemulsion) for different droplet sizes (water/AOT molar ratio wo=25 to 56) and concentrations (droplet weight fraction cw=2% to 20%). This allowed us to distinguish between contributions from individual scattering particles, e.g., droplets and cylinders to the total scattering intensity. The complete data set containing over 500 scattering curves could be interpreted by fitting the scattering of weighted sums of AOT covered water droplets, long cylinders, and inverse AOT micelles containing bound water only, to the experimental scatterin.
The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators

Abstract Motivation One avenue to address the paucity of clinically testable targets is to reinvestigate the druggable genome by tackling complicated types of targets such as Protein-Protein Interactions (PPIs). Given the challenge to target those interfaces with small chemical compounds, it has become clear that learning from successful examples of PPI modulation is a powerful strategy. Freely accessible databases of PPI modulators that provide the community with tractable chemical and pharmacological data, as well as powerful tools to query them, are therefore essential to stimulate new drug discovery projects on PPI targets. Results Here, we present the new version iPPI-DB, our manually curated database of PPI modulators. In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database. This interface was created to enable community contributions, whereby external experts can suggest new database entries. Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved. We added new PPI modulators, new PPI targets and extended our focus to stabilizers of PPIs as well. Availability and implementation The iPPI-DB server is available at https://ippidb.pasteur. fr The source code for this server is available at https://gitlab.pasteur. fr/ippidb/ippidb-web/ and is distributed under GPL licence (http://www.gnu.org/licences/gpl). Queries can be shared through persistent links according to the FAIR data standards. Data can be downloaded from the website as csv files. Supplementary information Supplementary data are available at Bioinformatics online.
Immobilized Hydroxynitrile Lyase: A Comparative Study of Recyclability

Hydroxynitrile lyase from cassava, Manihot esculenta, (MeHNL) catalyzes the formation of (S)‐cyanohydrins from HCN and aldehydes or ketones. Four differently immobilized MeHNLs were prepared: by noncovalent immobilization (celite R‐633), covalent immobilization (cross‐linked enzyme aggregates, CLEA), encapsulation [in a poly(vinyl alcohol) hydrogel Lentikats] and a combination of the above, an unusual immobilization, CLEA encapsulated in a poly(vinyl alcohol) hydrogel. A comparative study of the recyclability of each immobilized MeHNL was performed. Particular attention was paid to the stability and activity of the new immobilized MeHNL–CLEA–Lentikats and to the minimum enzyme loading required to achieve high yields and enantiomeric excesses. MeHNL–CLEA stability was slightly improved by encapsulation into Lentikats and good recyclability rates at low enzyme loading were obtained. However, MeHNL immobilized on celite R‐633 exhibited the best recyclability, giving >95 % conversion and an enantiomeric excess of 99 % during 12 cycles.
Dealing with an aging China—Delaying retirement or the second-child policy?

To tackle China’s rapidly aging population, a policy was framed by using overlapping generations (OLG) model and computable general equilibrium (CGE) model; the main objective was to successfully implement “second-child policy” and “delayed retirement age” for female or male workers. The 2012 census data was obtained from National Bureau of Statistics of China. Our research findings suggest that the economy can be improved in the short-term by delaying retirement age; however, Chinese economy would improve tremendously in the long run by implementing second-child policy. Compared to delayed retirement age, second-child policy would be more effective in improving the economy in China. In terms of industrial output, the three policies have a greater influence on labor-intensive industries, such as agriculture, light industry, finance, and service sector; the impact is less significant on construction and heavy industry. In terms of industrial import and export, these three policies have greatly influenced following industries: finance, electric power, and fossil energy. From a monetary perspective, these three policies can significantly improve household income; these three policies did not significantly impact both government and corporate incomes.
Preventive effects of influenza and pneumococcal vaccination in the elderly – results from a population-based retrospective cohort study

ABSTRACT Influenza and pneumococcal vaccinations are recommended in the elderly to reduce life-threatening complications like sepsis. Protection may be reduced with increasing age. We aimed to assess the effectiveness of both vaccines in the elderly by performing a retrospective cohort study of 138,877 individuals aged ≥60 y in Germany, who were insured in a large statutory health insurance (AOK PLUS). We used longitudinal claims data to classify individuals according to vaccination status 2008–2014, and assessed vaccine effectiveness (VE) in 2015 and 2016. Inverse probability weighting based on generalized propensity scores was used to adjust for systematic between-group differences. Influenza vaccination was associated with a reduction of hospital treatment in laboratory-confirmed influenza in 2015 (VE = 41.32 [95%CI 0.85, 65.26]), but had no significant impact on the overall influenza incidence. Complications of influenza (pneumonia and sepsis) were reduced in 2016. We found a rise in influenza-like illness and acute respiratory infections in both years and an increased 90-d mortality after hospital-treated pneumonia in vaccinees in 2015. Pneumococcal vaccination was effective in preventing hospital-treated pneumonia within the first and second year after vaccination (VE = 52.45 [13.31, 73.92] and 46.04 [5.46, 69.21], respectively), but had no impact on sepsis incidence or pneumonia mortality. Influenza and pneumococcal vaccination can prevent severe complications from influenza and hospital-treated pneumonia in the elderly, respectively. Vaccine effects differ between years and seasons and are partly difficult to interpret. Despite extensive efforts to adjust for between-group differences, residual bias cannot be ruled out, possibly explaining signals like increased ILI or pneumonia mortality.