Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene

Influenza A (H1N1) pdm09 virus emerged in North America in 2009 and has been established as a seasonal strain in humans. After an antigenic stasis of about six years, new antigenically distinct variants of the virus emerged globally in 2016 necessitating a change in the vaccine formulation for the first time in 2017. Herein, we analyzed thirty-eight HA sequences of influenza A (H1N1) pdm09 strains isolated in Kenya during 2015–2018 seasons, to evaluate their antigenic and molecular properties based on the HA1 sub-unit. Our analyses revealed that the A (H1N1) pdm09 strains that circulated in Kenya during this period belonged to genetic clade 6B, subclade 6B.1 and 6B.2. The Kenyan 2015 and 2016 isolates differed from the vaccine strain A/California/07/2009 at nine and fourteen antigenic sites in the HA1 respectively. Further, those isolated in 2017 and 2018 correspondingly varied from A/Michigan/45/2015 vaccine strain at three and fifteen antigenic sites. The predicted vaccine efficacy of A/California/07/2009 against Kenyan 2015/2016 was estimated to be 32.4% while A/Michigan/45/2015 showed estimated vaccine efficacies of 39.6% - 41.8% and 32.4% - 42.1% against Kenyan 2017 and 2018 strains, respectively. Hemagglutination-inhibition (HAI) assay using ferret post-infection reference antiserum showed that the titers for the Kenyan 2015/2016 isolates were 2–8-fold lower compared to the vaccine strain. Overall, our results suggest the A (H1N1) pdm09 viruses that circulated in Kenya during 2015/2016 influenza seasons were antigenic variants of the recommended vaccine strains, denoting sub-optimal vaccine efficacy. Additionally, data generated point to a swiftly evolving influenza A (H1N1) pdm09 virus in recent post pandemic era, underscoring the need for sustained surveillance coupled with molecular and antigenic analyses, to inform appropriate and timely influenza vaccine update.
ALSUntangled 53: Carnitine supplements

ISSN: 2167-8421 (Print) 2167-9223 (Online) Journal homepage: https://www.tandfonline. com/loi/iafd20 ALSUntangled 53: Carnitine supplements THE ALSUNTANGLED GROUP To cite this article: THE ALSUNTANGLED GROUP (2020): ALSUntangled 53: Carnitine supplements, Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, DOI: 10.1080/21678421.2020. 1726565 To link to this article: https://doi.org/10.1080/21678421.2020. 1726565
Hospital adoption of multiple health information exchange approaches and information accessibility

OBJECTIVE Hospital engagement in electronic health information exchange (HIE) has increased over recent years. We aimed to 1) determine the change in adoption of 3 types of information exchange: secure messaging, provider portals, and use of an HIE; and 2) to assess if growth in each approach corresponded to increased ability to access and integrate patient information from outside providers. METHODS Panel analysis of all nonfederal, acute care hospitals in the United States using hospital- and year-fixed effects. The sample consisted of 1917 hospitals that responded to the American Hospital Association Information Technology Supplement every year from 2014 to 2016. RESULTS Adoption of each approach increased by 9-15 percentage points over the study period. The average number of HIE approaches used by each hospital increased from 1.0 to 1.4. Adoption of each approach was associated with increased likelihood that providers routinely had necessary outside information of 4.2-12.7 percentage points and 4.5-13.3 percentage points increase in information integration. Secure messaging was associated with the largest increase in both. Adoption of 1 approach increased the likelihood of having outside information by 10.3 percentage points, while adopting a second approach further increased the likelihood by 9.5 percentage points. Trends in number of approaches and integration were similar. DISCUSSION/CONCLUSION No single HIE tool provided high levels of usable, integrated health information. Instead, hospitals benefited from adopting multiple tools. Policy initiatives that reduce the complexity of enabling high value HIE could result in broader adoption of HIE and use of information to inform care.
Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Longan (Dimocarpus longan L.)

Auxin response factor (ARF) is the key regulator involved in plant development. Despite their physiological importance identified in various woody plants, the functions of ARF genes in longan were still not clear. In this study, 17 longan ARF genes (DlARF) were identified using the reference longan genome data. According to the phylogenetic relationships among longan, Arabidopsis and apple, DlARFs were divided into four classes. Most DlARFs showed a closer relationship with ARFs from apple than those from Arabidopsis. The analysis of gene structure and domain revealed high similarity of different ARF genes in the same class. Typical features of B3-type DNA binding domain (DBD) motif, Auxin Resp motifs, and a highly conserved C-terminal Phox and Bem1 (PB1) domain were present in all DlARFs except for DlARF-2,-3,-13 which lacked PBI domain. Expression profiles of 17 DlARF genes in longan different tissues showed that some DlARF genes were tissues-specific genes. Analysis of three longan transcriptomes showed seven DlARFs (DlARF-1,-2,-6,-8,-9,-11,-16) had higher expression levels during floral bud differentiation of common longan and in the buds of ‘Sijimi’, suggesting these genes may promote floral bud differentiation in longan. Further qPCR analysis showed that among seven DlARF genes, the expression levels of DlARF-2,-6,-11,-16 increased significantly during the physiological differentiation stage of longan floral buds, confirming that they may play a role in flowering induction. Promoter sequence analysis revealed cis-elements related to flowering induction such as low-temperature responsiveness motif and circadian control motif. Motifs linked with hormone response for instance Auxin, MeJA, Gibberellin, and Abscisic acid were also found in promoters. This study provides a comprehensive overview of the ARF gene family in longan. Our findings could provide new insights into the complexity of the regulation of ARFs at the transcription level that may be useful to develop breeding strategies to improve development or promote flowering in longan.
High-Performance Pt-Co Nanoframes for Fuel Cell Electrocatalysis.

Pt-based alloy catalysts are promising candidates for fuel cell applications, especially for cathodic oxygen reduction reaction (ORR) and anodic methanol oxidation reaction (MOR). Rational design of composition and morphology is crucial to promoting the catalytic performances. Here, we report the synthesis of Pt-Co nanoframes via chemical etching of Co from solid rhombic dodecahedra. The obtained Pt-Co nanoframes exhibit remarkable ORR and MOR properties. The ORR mass activity in acidic electrolyte is as high as 0.40 A mgPt-1 at 0.95 VRHE, which is 4 times higher than that of commercial Pt/C catalyst. The long-term ORR durability also stands out with 0.34 A mgPt-1 maintained after 10,000 potential cycles, accredited to negligible Co dissolution. Furthermore, the MOR mass activity of the nanoframes in alkaline media is up to 4.28 A mgPt-1, which is 4-fold enhancement compared with that of commercial Pt/C. Experimental studies indicate that the weakened binding of intermediate carbonaceous poison contributes to the enhanced MOR activity. More impressively, the Pt-Co nanoframes also show remarkable structural stability after the electrocatalysis. This work provides an effective strategy to produce high-performance Pt-Co nanoframes for fuel-cell-related applications.
A New Edge Patch with Rotation Invariance for Object Detection and Pose Estimation

Local patch-based methods of object detection and pose estimation are promising. However, to the best of the authors’ knowledge, traditional red-green-blue and depth (RGB-D) patches contain scene interference (foreground occlusion and background clutter) and have little rotation invariance. To solve these problems, a new edge patch is proposed and experimented with in this study. The edge patch is a local sampling RGB-D patch centered at the edge pixel of the depth image. According to the normal direction of the depth edge, the edge patch is sampled along a canonical orientation, making it rotation invariant. Through a process of depth detection, scene interference is eliminated from the edge patch, which improves the robustness. The framework of the edge patch-based method is described, and the method was evaluated on three public datasets. Compared with existing methods, the proposed method achieved a higher average F1-score (0.956) on the Tejani dataset and a better average detection rate (62%) on the Occlusion dataset, even in situations of serious scene interference. These results showed that the proposed method has higher detection accuracy and stronger robustness.
Changes in the Association between European Workers’ Employment Conditions and Employee Well-Being in 2005, 2010 and 2015

The aim of this paper is to study whether there is a change in the association between employment conditions and European employees’ well-being at three different time points (the years 2005, 2010 and 2015), characterized by different socio-economic contexts. We based our study on the European Working Conditions Survey. Logistic regressions were performed by adjusting for gender, age, level of education, seniority, occupation, establishment size, activity sector and economic activity. Adjusted odds ratios (ORadj) and 95% confidence intervals (95% CI) are reported. In general, the association between employment conditions (type of employment contract, supervising, weekly working hours, long working hours, other paid jobs, working at weekends or doing shifts) and well-being indicators (anxiety, fatigue and dissatisfaction) seemed to continue being harmful, or had even changed for the worse since 2005. The paper briefly discusses the possible reasons for this situation and calls for future research on the relation between well-being and irregular type of contracts, self-employment, supervising others or hours worked per week. Some implications in public health policies are also discussed.
CD73 Blockade Promotes Dendritic Cell Infiltration of Irradiated Tumors and Tumor Rejection

Radiation-induced adenosine production is identified as a barrier that limits radiotherapy-induced antitumor immune responses. Antibodies to CD73 that block adenosine generation could be used in combination with radiotherapy and immune checkpoint blockade to improve response to radiation therapy. The ability of focal radiotherapy to promote priming of tumor-specific CD8+ T cells and increase responses to immunotherapy is dependent on infiltration of the tumor by Batf3-dependent conventional dendritic cell type 1 (cDC1) cells. Such infiltration is driven by radiotherapy-induced IFN type I (IFN-I). Other signals may also modulate cDC1 infiltration of irradiated tumors. Here we found increased expression of adenosine-generating enzymes CD38 and CD73 in irradiated mouse and human breast cancer cells and increased adenosine in mouse tumors following radiotherapy. CD73 blockade alone had no effect. CD73 blockade with radiotherapy restored radiotherapy-induced cDC1 infiltration of tumors in settings where radiotherapy induction of IFN-I was suboptimal. In the absence of radiotherapy-induced IFN-I, blockade of CD73 was required for rejection of the irradiated tumor and for systemic tumor control (abscopal effect) in the context of cytotoxic T-lymphocyte–associated protein 4 blockade. These results suggest that CD73 may be a radiation-induced checkpoint, and that CD73 blockade in combination with radiotherapy and immune checkpoint blockade might improve patient response to therapy.
Characterization of E. coli and Salmonella spp. isolates associated with omphalitis in baby chicks

ARTICLE INFO Omphalitis is a major cause of increased first week-chick mortality. Omphalitis, navel-yolk sac infection, is a hatchery-born disease, and also known as ‘mushy chick disease’ or ‘navel ill’. It is a common disease of chicks and poults, often artificially hatched chicks, causing high losses in the brooding period, as a bacterium penetrates the porous egg shell. As incubation conditions are suitable for bacterial growth and incubating eggs as well, various bacteria, such as E. coli, staphylococci, Proteus, Clostridium fecali and Pseudomonas may be involved in the yolk sac infection. The present study aimed to determine bacterial causes of omphalitis through isolation and identification of such pathogens. Therefore, samples from 216 yolk sacs were collected from chicks with unabsorbed yolk materials that could even smell putrid. Among those, 196 (90.7%) were positive; 135 (62.5%) harboured single bacterial strains and 61 (28.2%) had mixed infections. The most prevalent single bacterial isolates were E. coli (110 isolates) and P. aeruginosa (11 isolates). Meanwhile, the most predominant mixed bacterial strains were E. coli with Salmonella spp. (16 isolates; 7.4%) and E. coli with P. aeruginosa (13 isolates; 6%). Other mixed infections were found in low percentages. Most E. coli strains were Congo red-positive and non-haemolytic. Different E. coli serogroups were serologically identified including O27 (4 isolates; 20%), O157 (3isolates; 15%), O26 (3 isolates; 15%) and one isolate of each of the following; O78, O6, O125, O44, O15, O115, O25, O168, O112 and O63 (each of 5%). Different Salmonella serogroups were identified including S. cremieu (2 isolates) and one isolate of each of the following S. enteritidis, S. blegdam, S. senftenberg, S. kingston and S. emek. Isolated bacteria differed in Article history:
Comparative In Vitro Resistance of Human Periodontal Bacterial Pathogens to Tinidazole and Four Other Antibiotics

The in vitro resistance of selected red/orange complex periodontal pathogens to tinidazole was compared with four other antibiotics. Subgingival biofilm samples from 88 adults with severe periodontitis were anaerobically incubated on enriched Brucella blood agar with and without supplementation with tinidazole (16 mg/L), metronidazole (16 mg/L), amoxicillin (8 mg/L), doxycycline (4 mg/L), or clindamycin (4 mg/L). Growth of Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia/nigrescens, Parvimonas micra, Fusobacterium nucleatum, Streptococcus constellatus, or Campylobacter rectus on antibiotic-supplemented plates indicated their in vitro antibiotic resistance. Tinidazole inhibited all test species, except P. intermedia/nigrescens, P. micra, and S. constellatus in 3.8%, 10.2%, and 88.9% of species-positive patients, respectively. Significantly fewer patients yielded tinidazole-resistant test species, and had significantly lower subgingival proportions of tinidazole-resistant organisms, than patients with amoxicillin, doxycycline, or clindamycin-resistant species, but not those with metronidazole-resistant strains. Joint in vitro species resistance to tinidazole and amoxicillin, or metronidazole and amoxicillin, was rare. Tinidazole performed in vitro similar to metronidazole, and markedly better than amoxicillin, doxycycline, or clindamycin, against fresh clinical isolates of red/orange complex periodontal pathogens. As a result of its similar antimicrobial spectrum, and more convenient once-a-day oral dosing, tinidazole should be considered in place of metronidazole for systemic periodontitis drug therapy.
Performance Analysis of Boosting Classifiers in Recognizing Activities of Daily Living

Physical activity is essential for physical and mental health, and its absence is highly associated with severe health conditions and disorders. Therefore, tracking activities of daily living can help promote quality of life. Wearable sensors in this regard can provide a reliable and economical means of tracking such activities, and such sensors are readily available in smartphones and watches. This study is the first of its kind to develop a wearable sensor-based physical activity classification system using a special class of supervised machine learning approaches called boosting algorithms. The study presents the performance analysis of several boosting algorithms (extreme gradient boosting—XGB, light gradient boosting machine—LGBM, gradient boosting—GB, cat boosting—CB and AdaBoost) in a fair and unbiased performance way using uniform dataset, feature set, feature selection method, performance metric and cross-validation techniques. The study utilizes the Smartphone-based dataset of thirty individuals. The results showed that the proposed method could accurately classify the activities of daily living with very high performance (above 90%). These findings suggest the strength of the proposed system in classifying activity of daily living using only the smartphone sensor’s data and can assist in reducing the physical inactivity patterns to promote a healthier lifestyle and wellbeing.
Alcohol Dependence and Reproductive Onset in Women, Updated: Analyses of Research and State-Level Administrative Data.

OBJECTIVE The present study updates prior research, incorporating state-level administrative data to examine associations between self-reported history of alcohol dependence and birth record-derived reproductive onset, the latter assessed through peak childbearing years. METHOD Participants included 542 African ancestry (AA) and 2,928 European or other ancestry (EA) female twins ascertained through Missouri birth records and recruited as part of a birth cohort study of like-sex female pairs born between 1975 and 1985. Analyses were limited to twins for whom residence in Missouri when of reproductive age could be documented, including twins who left Missouri but later returned. Cox proportional hazards regression models were estimated predicting age at first childbirth from history of alcohol dependence, separately for AA and EA twins, without and with adjustment for sociodemographic characteristics, comorbid psychopathology and other substance involvement, overweight/obesity status, and family-of-origin and childhood risk factors. RESULTS Among EA twins, alcohol dependence predicted both early and delayed childbearing; in adjusted models, alcohol dependence was associated with overall delayed childbearing. Associations between alcohol dependence and reproductive onset were nonsignificant among AA twins. CONCLUSIONS Findings for EA twins are consistent with the broader literature indicating increased risk of teen motherhood associated with early-onset and problem drinking, but suggest that this may be explained by other correlated risk factors. The more robust finding, confirming relatively recent research, is of delayed childbearing associated with alcohol dependence.
PD-1 Deficiency Promotes Macrophage Activation and Th1/Th17 Response in Pneumocystis Pneumonia.

Pneumocystis is an unusual, opportunistic fungal pathogen capable of causing Pneumocystis pneumonia (PCP) in immunocompromised hosts. Though PCP was discovered more than 100 years ago, its pathogenesis remains unclear. The inhibitory receptor programmed death 1 (PD-1), a negative regulator of activated T cells, has been reported to take part in tumor escape, immune tolerance, and infection immunity. In this study, we examined the role of the PD-1/programmed death-ligand 1 (PD-L1) pathway in PCP patients and mice. The expression levels of PD-1/PD-L1 in PCP patients and mice were measured by real-time PCR and flow cytometry. The effects of PD-1 deficiency are demonstrated using wild-type and PD-1-/- mice. Our data show that Pneumocystis infection promotes PD-1/PD-L1 expression; PD-1 deficiency enhances the phagocytic function of macrophages and the pulmonary Th1/Th17 response, which might contribute to Pneumocystis clearance; PD-1 deficiency affects the polarization of macrophages. PCP mice treated with anti-PD-1 antibody showed improved pulmonary clearance of Pneumocystis. Collectively, our results demonstrate that the PD-1/PD-L1 pathway plays a role in regulating the innate and adaptive immune responses, suggesting that manipulation of this pathway may constitute an immunotherapeutic strategy for PCP.
Universal Dermal Microbiome in Human Skin

Human skin microbiota is thought to be unique according to the individual's lifestyle and genetic predisposition. This is true for the epidermal microbiota, while our findings demonstrate that the dermal microbiota is universal between healthy individuals. The preserved dermal microbial community is compositionally unique and functionally distinct to the specific environment in the depth of human skin. It is expected to have direct contact with the immune response of the human host, and research in the communication between host and microbiota should be targeted to this cutaneous compartment. This novel insight into specific microbial adaptation can be used advantageously in the research of chronic disorders and infections of the skin. It can enlighten the alteration between health and disease to the benefit of patients suffering from long-lasting socioeconomic illnesses. ABSTRACT Human skin microbiota has been described as a “microbial fingerprint” due to observed differences between individuals. Current understanding of the cutaneous microbiota is based on sampling the outermost layers of the epidermis, while the microbiota in the remaining skin layers has not yet been fully characterized. Environmental conditions can vary drastically between the cutaneous compartments and give rise to unique communities. We demonstrate that the dermal microbiota is surprisingly similar among individuals and contains a specific subset of the epidermal microbiota. Variability in bacterial community composition decreased significantly from the epidermal to the dermal compartment but was similar among anatomic locations (hip and knee). The composition of the epidermal microbiota was more strongly affected by environmental factors than that of the dermal community. These results indicate a well-conserved dermal community that is functionally distinct from the epidermal community, challenging the current dogma. Future studies in cutaneous disorders and chronic infections may benefit by focusing on the dermal microbiota as a persistent microbial community. IMPORTANCE Human skin microbiota is thought to be unique according to the individual's lifestyle and genetic predisposition. This is true for the epidermal microbiota, while our findings demonstrate that the dermal microbiota is universal between healthy individuals. The preserved dermal microbial community is compositionally unique and functionally distinct to the specific environment in the depth of human skin. It is expected to have direct contact with the immune response of the human host, and research in the communication between host and microbiota should be targeted to this cutaneous compartment. This novel insight into specific microbial adaptation can be used advantageously in the research of chronic disorders and infections of the skin. It can enlighten the alteration between health and disease to the benefit of patients suffering from long-lasting socioeconomic illnesses.
T-Type Calcium Channels: A Potential Novel Target in Melanoma

T-type calcium channels (TTCCs) are overexpressed in several cancers. In this review, we summarize the recent advances and new insights into TTCC biology, tumor progression, and prognosis biomarker and therapeutic potential in the melanoma field. We describe a novel correlation between the Cav3.1 isoform and the increased basal autophagy in BRAFV600E-mutant melanomas and after acquired resistance to BRAF inhibitors. Indeed, TTCC blockers reduce melanoma cell viability and migration/invasion in vitro and tumor growth in mice xenografts in both BRAF-inhibitor-sensitive and -resistant scenarios. These studies open a new, promising therapeutic approach for disseminated melanoma and improved treatment in BRAFi relapsed melanomas, but further validation and clinical trials are needed for it to become a real therapeutic option.