Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010–2015

In this retrospective study, we used whole-genome sequencing (WGS) to delineate transmission dynamics, characterize drug-resistance markers, and identify risk factors of transmission among Papua New Guinea residents of the Torres Strait Protected Zone (TSPZ) who had tuberculosis diagnoses during 2010–2015. Of 117 isolates collected, we could acquire WGS data for 100; 79 were Beijing sublineage 2.2. 1.1, which was associated with active transmission (odds ratio 6.190, 95% CI 2.221–18.077). Strains were distributed widely throughout the TSPZ. Clustering occurred more often within than between villages (p = 0.0013). Including 4 multidrug-resistant tuberculosis isolates from Australia citizens epidemiologically linked to the TSPZ into the transmission network analysis revealed 2 probable cross-border transmission events. All multidrug-resistant isolates (33/104) belonged to Beijing sublineage 2.2. 1.1 and had high-level isoniazid and ethionamide co-resistance; 2 isolates were extensively drug resistant. Including WGS in regional surveillance could improve tuberculosis transmission tracking and control strategies within the TSPZ.
Influence of different stages of corpus luteum on ovary size, oocytes grades and follicular population in Indian buffaloes

The aim of this study was to evaluate the effect of different stages of corpus luteum on ovary size, oocytes grades and follicular population. A total of 109 buffalo ovaries were collected from the slaughterhouse and transported to the laboratory for determination of ovaries weight, length, width, thickness, follicular population and oocytes grades. The results obtained revealed that the effect of types of CL on ovary weight and size showed a significant difference in the type of CL groups with ovary weight and ovary size. Ovaries having CL in late-stage showed the highest mean of ovary weight, length, width and thickness over the CL in the early and middle stage. Moreover, the results showed no significantly different in the type of CL groups with follicular population and oocytes grades.
HIV/AIDS sero-prevalence and socioeconomic status: Evidence from Uganda

Although Uganda reported large reductions in HIV/AIDS prevalence during the 1990s, recent evidence suggests that country’s rate of new HIV infections is on the rise. This study explores the factors that are correlated with sexual behavior and the risk of HIV infection using a unique dataset of 19,500 individuals from the 2011 Uganda AIDS Indicator Survey. This survey tested individuals 15-49 years of age for sexually transmitted infections, including the HIV virus. The same survey also collected background information for all tested individuals. This information is similar to what is collected in a typical demographic and health survey (DHS). We estimate probit models for the correlates of risky sexual behaviors that can lead to HIV infection such as: having concurrent sexual partners, no-condom use, and alcohol use during sex. In addition, we examine correlates of having been tested for HIV prior to the survey. Also, we estimate models for correlates of the risk of testing HIV positive as well as the self-assessed risks of contracting HIV. We find that higher education attainment and access to health facilities are important for adopting safe sexual behaviors as well as the reducing the risk of testing HIV positive. Among HIV infected couples, we find that women have a higher rate of discordance which is at odds with the low rates of self-reported extra marital sexual behavior.
DCT4 - a new member of the dicarboxylate transporter family in C4 grasses

Malate transport shuttles atmospheric carbon into the Calvin-Benson cycle during NADP-ME C4 photosynthesis. Previous characterizations of several plant dicarboxylate transporters (DCT) showed that they efficiently exchange malate across membranes. Here we identify and characterize a previously unknown member of the DCT family, DCT4, in Sorghum bicolor. We show that SbDCT4 exchanges malate across membranes and its expression pattern is consistent with a role in malate transport during C4 photosynthesis. SbDCT4 is not syntenic to the characterized photosynthetic gene ZmDCT2, and an ortholog is not detectable in the maize reference genome. We found that the expression patterns of DCT family genes in the leaves of Z. mays, and S. bicolor varied by cell type. Our results suggest that sub-functionalization of members of the DCT family for the transport of malate into the bundle sheath (BS) plastids occurred during the process of independent recurrent evolution of C4 photosynthesis in grasses of the PACMAD clade. This study confirms the value of using both syntenic information and gene expression profiles to assign orthology in evolutionarily related genomes.
Design and Validation of Multichannel Wireless Wearable SEMG System for Real-Time Training Performance Monitoring

Monitoring of training performance and physical activity has become indispensable these days for athletes. Wireless technologies have started to be widely used in the monitoring of muscle activation, in the sport performance of athletes, and in the examination of training efficiency. The monitorability of performance simultaneously in the process of training is especially a necessity for athletes at the beginner level to carry out healthy training in sports like weightlifting and bodybuilding. For this purpose, a new system consisting of 4 channel wireless wearable SEMG circuit and analysis software has been proposed to detect dynamic muscle contractions and to be used in real-time training performance monitoring and analysis. The analysis software, the Haar wavelet filter with threshold cutting, can provide performance analysis by using the methods of moving RMS and %MVC. The validity of the data obtained from the system was investigated and compared with a biomedical system. In this comparison, 90.95% ± 3.35 for left biceps brachii (BB) and 90.75% ± 3.75 for right BB were obtained. The output of the power and %MVC analysis of the system was tested during the training of the participants at the gym, and the training efficiency was measured as 96.87% ± 2.74.
Water scavenger beetles in rotten cacti: a review of Agna with the description of a new species from Mexico (Coleoptera: Hydrophilidae: Sphaeridiinae)

The terrestrial hydrophilid genus Agna Smetana (tribe Megasternini), specialized in rotten cacti, is redescribed and illustrated. Known species are diagnosed and a new one, A. zaragozai sp. nov., is described from central Mexico (Hidalgo, Puebla, and Oaxaca) and its molecular barcode is provided. Other species of Hydrophilidae known to have been collected in cacti are listed and commented. Dactylosternum cacti (LeConte) (Coelostomatini) is recorded for the first time from Mexico and Cryptopleurum impressum Sharp (Megasternini) is recorded for the first time from the Mexican states of Jalisco and San Luis Potosi.
Utilization of dried poultry manure in cross bred heifers.

Twelve cross-bred (Deoni x Holstein Friesian) heifers (13m; 180±32 kg) were randomly divided into 3 equal groups and fed rations containing 0(T1), 15 (T2) and 30 (T3) percent dried poultry manure (DPM) for 90 d. There were no significant differences in the average daily DM intake and nutrient digestibilities among control and DPM susbtituted treatment groups. There were no significant differences in the DCP content of three experimental rations. However, the TDN content of T3 ration was significantly (P<0.05) lower than the T1 and T2 rations.
Effect of Indigofera oblongifolia on the Hepatic Oxidative Status and Expression of Inflammatory and Apoptotic Genes during Blood-Stage Murine Malaria

Malaria is a dangerous disease spread across several countries. Recent studies have focused on medicinal plants to discover alternative agents to the currently used drugs for malaria treatment. Here, we investigated the potential role of Indigofera oblongifolia leaf extract (IE) on hepatic inflammation in mice with Plasmodium chabaudi-infected erythrocytes. Female C57BL/6 mice were divided into three groups. The first group served as a control noninfected group, while the second and third groups were intraperitoneally injected with 106 erythrocytes parasitized by P. chabaudi. Mice from the third group were treated daily with a dose of 100 mg/kg of IE for 7 days. IE significantly reduced the number of leukocytes and apoptotic cells. The numbers of CD68-positive cells decreased in the livers of mice from the treatment group. Moreover, IE raised the hepatic antioxidant levels (glutathione and catalase) and reduced the levels of hepatic oxidative stress markers (malondialdehyde, nitric oxide, and reactive oxygen species). IE regulated some functions of the genes related to immune responses, including apoptotic genes (B-cell lymphoma-2, Bax, and caspase-3) and cytokine genes (interleukin-1β (IL-1β), IL-6, interferon-γ, and tumor necrosis factor-α). Therefore, IE exerts significant effects against malaria and protects the liver from injury caused by P. chabaudi via antioxidant and anti-inflammatory ways.
A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses

Endogenous retroviruses (ERVs) can be thought of as host genomic fossils of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFV) have previously been discovered in mammals, amphibians and fish. Here we report a novel endogenous foamy virus, named SpuEFV, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that SpuEFV has likely co-diverged with its host over a period of many millions of years. The discovery of SpuEFV fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
Essentials Of Oral Pathology And Oral Medicine

Principles of Investigation and Diagnosis Section 1 Hard Tissue Pathology: Disorders of Development of the Teeth and Related Tissues. Dental Caries. Pulpitis, Apical Periodontitis, Resorption, Hypercementosis. Gingivitis and Periodontitis. Major Infections of the Mouth, Jaws and Perioral Tissues. Cysts of the Jaws. Odontogenic Tumours and Tumour-Like Lesions of the Jaws. Non-Odontogenic Tumours of the Jaws. Genetic, Metabolic and Other Non-Neoplastic Bone Diseases. The Temporomandibular Joints and Periarticular Tissues Section Ii Soft Tissue Disease: Diseases of the Oral Mucosa: Infective Stomatitis. Diseases of the Oral Mucosa: Non-Infective Stomatitis. Tongue Disorders. Benign Chronic White Mucosal Lesions. Oral Premalignancy. Oral Cancer. Neoplastic and Non-Neoplastic Diseases of Salivary Glands. Common Benign Mucosal Swellings. Soft Tissue (Mesenchymal) Neoplasms and Lymphomas. Melanoma and Other Pigmented Lesions Section Iii the Medically Compromised Patient: Anaemias and Leukaemias. Haemorrhagic Diseases. Immunodeficiency Diseases and Acquired Immune Deficiency Syndrome. Immunologically-Mediated Diseases. Cervical Lymphadenopathy. Cardiavascular Disease. Respiratory Tract Disease. Gastrointestinal and Liver Disease. Nutritional Deficiencies. Endocrine Disease and Pregnancy. Renal Disease. Handicapping Disorders. Pain, Anxiety and Neurological Disorders. Complications of Systemic Drug Treatment. Emergencies in Dental Practice.
Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography

Abstract Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here, we relaxed this strong assumption and allowed for analytic integration of uncertainty for discrete virus phylogeography. We used automatic language processing methods to find and assign uncertainty to alternative potential locations. We considered two influenza case studies: H5N1 in Egypt; H1N1 pdm09 in North America. For each, we implemented scenarios in which 25 per cent of the taxa had different amounts of sampling uncertainty including 10, 30, and 50 per cent uncertainty and varied how it was distributed for each taxon. This includes scenarios that: (i) placed a specific amount of uncertainty on one location while uniformly distributing the remaining amount across all other candidate locations (correspondingly labeled 10, 30, and 50); (ii) assigned the remaining uncertainty to just one other location; thus ‘splitting’ the uncertainty among two locations (i.e. 10/90, 30/70, and 50/50); and (iii) eliminated uncertainty via two predefined heuristic approaches: assignment to a centroid location (CNTR) or the largest population in the country (POP). We compared all scenarios to a reference standard (RS) in which all taxa had known (absolutely certain) locations. From this, we implemented five random selections of 25 per cent of the taxa and used these for specifying uncertainty. We performed posterior analyses for each scenario, including: (a) virus persistence, (b) migration rates, (c) trunk rewards, and (d) the posterior probability of the root state. The scenarios with sampling uncertainty were closer to the RS than CNTR and POP. For H5N1, the absolute error of virus persistence had a median range of 0.005–0.047 for scenarios with sampling uncertainty—(i) and (ii) above—versus a range of 0.063–0.075 for CNTR and POP. Persistence for the pdm09 case study followed a similar trend as did our analyses of migration rates across scenarios (i) and (ii). When considering the posterior probability of the root state, we found all but one of the H5N1 scenarios with sampling uncertainty had agreement with the RS on the origin of the outbreak whereas both CNTR and POP disagreed. Our results suggest that assigning geospatial uncertainty to taxa benefits estimation of virus phylogeography as compared to ad-hoc heuristics. We also found that, in general, there was limited difference in results regardless of how the sampling uncertainty was assigned; uniform distribution or split between two locations did not greatly impact posterior results. This framework is available in BEAST v.1. 10. In future work, we will explore viruses beyond influenza. We will also develop a web interface for researchers to use our language processing methods to find and assign uncertainty to alternative potential locations for virus phylogeography.
THE TOPICAL ANESTHESIA WITH EMLA CREAM IN CHILDREN : A CASE REPORT

A number of techniques may be employed to reduce the discomfort of syringe or needle for dental care. The use of topical anesthesia is one such method. Topical anesthetics are applied to alleviate pain during many clinical procedures, such as injection of local infiltration anesthetics, primary tooth extraction, X-ray taking of sensitive patients, reducing gag reflex prior to impression taking. In children, placement of a rubber dam clamp, however, may cause significant discomfort for purpose of pit and fissure sealant and preventive resin restoration(PRR). A topical anesthetic would be beneficial to aid in rubber dam placement for this purpose. It has been suggested that all intra-oral topical anesthetics are equally effective on reflected mucosa, however EMLA(an acronym for eutectic mixture of local anesthetics), which was developed in the 1980s and produces surface anesthesia of skin, has been shown to be more effective than conventional topical anesthetics when used on attached gingivae. This report is topical anesthesized 4 case by EMLA cream, who showed better effect in reducing the pain of infiltration anesthesia, extraction of deciduous teeth, rubber dam clamp placement and reducing the pain of preformed crown adaptation.
A Study on Self Management, Hemoglobin A1c (HbA1c), and Perceived Health Status for the Type II Diabetes Patients

Purpose: This study is conducted to examine the relationship among self management, HbA1c, and perceived health status of type II diabetes patients in community health department. Methods: Data were collected from 93 type II diabetes patients who are registered at five community health center using comprehensive survey, modified self care behavior, blood glucose and HbA1c were assessed by nurses. The data was analyzed by the SPSS (14.0) computer program, and it included descriptive statistics, t-test, ANOVA, and pearson’s correlation coefficient. Results: There was significant relationship between perceived health status and HbA1c (r= -.252, p=.015). There was significant relationship between self management and HbA1c (r=-.279, p=.007). Conclusion: In order to control blood glucose in the type II diabetes patients, it is necessary to develop supportive self management programs by considering perceived health status
An Improved Hashing Method for Image Retrieval Based on Deep Neural Networks

Hashing algorithm projects the vector of features onto the binary space that generate the binary codes to reduce calculating time. Thus Hashing Algorithm is widely used to improve retrieval efficiency in traditional image retrieval methods based on Deep neural networks (DNNs). In this paper, we extract the feature vectors whose elements between 0 and 1 by DNNs and linear scaling method, then we define the mean of each column vector of the matrix consisted of these feature vectors as threshold to create corresponding hashing codes after two-stages binarization. Since threshold brings major effect to the preservation of the similarity between images, during this process, the two-stages binarization play two important roles: 1) optimizing thresholds; 2) optimizing hash codes. The promising experimental results on public available Cifar-10 database show that the proposed approach achieve higher precision compared with the state-of-the-art hashing algorithms.
Loanword adaption in Persian: A Core-Periphery model approach

This study discusses the adaptation of loanwords in Persian from donor languages of Arabic, French and English. The main claim is that loanwords adapt to the host language phonology based on the duration of the time they have been used in that language (Kemmer 2017). Thus, I propose that Arabic loans which are borrowed earlier are more nativized than recent loans, like Russian, French and English words. Compared to the former studies (Shademan 2002; Perry 2005, 2011; among others), this is the first account that aims to show the hierarchical and gradual nativization process of loans in Persian by use of Core-Periphery model (Itô and Mester 1999). This model categorizes words from core stratum to periphery stratum based on the satisfaction of constraints in the host language as systematic comparison criteria of older loans with recent ones. In this study I show that the Persian lexicon is stratified into three strata: core, middle and periphery. This lexicon stratification reflects the gradual nativization of loanwords where the core stratum includes frequent native items, the middle stratum includes older loans (Arabic) and the periphery stratum includes recent loans (Russian, French and English). Furthermore, this paper shows that highly frequent Arabic loans satisfying all constraints have become completely nativized and thus are categorized as part of the core showing the great influence of the donor language.
Long-term psychosocial impact of venous thromboembolism: a qualitative study in the community

Objectives Venous thromboembolism (VTE) is a serious, potentially traumatic, life-threatening condition and a major cause of mortality and morbidity. The aim of this study was to obtain detailed understandings of the impact of VTE and examine individual’s experiences over the first year since a first-time VTE. Design A longitudinal qualitative interview study using inductive thematic analysis. This study presents follow-up data for 11 participants, first interviewed 6 months following a first-time VTE. Setting Outpatients recruited from a community haematology clinic in a UK District General Hospital. Participants Eleven participants (seven females and four males) recruited from a community haematology clinic. Participants had experienced a first-time VTE and participated in qualitative interviews 3 months previously. Intervention Audio-recorded semistructured interviews with a sample of 11 participants who experienced a first-time deep vein thrombosis or pulmonary embolism within the previous year. Interviews were transcribed and analysed using inductive thematic analysis. Results Four overarching themes were identified: life changing and forever changed, the trauma of care, ‘thrombo-neuroses’ and through adversity comes growth. Theme content varied according to age and developmental stage, presence of VTE symptoms and the experience of diagnosis. Conclusions The data demonstrate the psychosocial impact of VTE and its diagnosis as physically and psychologically challenging, and individuals reported being forever changed by the experience. Participants’ reported continued high levels of trauma and anxiety symptoms, triggered by physical (eg, symptoms) and psychological (eg, health anxiety, negative emotions) reminders of VTE. Wider primary care service issues including misdiagnosis maintained negative emotions and health anxiety with implications for relationships with professionals. Targeted clinical interventions to better identify and support individuals at risk of distress and enhance psychological well-being and reduce distress are discussed.
Local Extinction of Bull Kelp (Durvillaea spp.) Due to a Marine Heatwave

Detailed research has documented gradual changes to biological communities attributed to increases in global average temperatures. However, localized and abrupt temperature anomalies associated with heatwaves may cause more rapid biological changes. We analysed temperature data from the South Island of New Zealand and investigated whether the hot summer of 2017/18 affected species of bull kelp, Durvillaea antarctica, D. poha and D. willana. Durvillaea spp. are large iconic seaweed that inhabit the low intertidal zone of exposed coastlines, where they underpin biodiversity and ecosystem functioning. Sea surface temperatures during the summer of 2017/18 included the strongest marine heatwaves recorded in 38 years of existing oceanic satellite data for this region. Air temperatures were also high, and, coupled with small wave heights, resulted in strong desiccation stress during daytime low tides. Before-After analysis of drone images of four reef platforms (42, 42, 44 and 45 ˚S) was used to evaluate changes to bull kelp over the hot summer. Bull kelp loss varied among species and reefs, with the greatest (100%) loss of D. poha at Pile Bay in Lyttelton Harbour (44 ˚S). In Pile Bay, sea surface temperature exceeded 23 ˚C and air temperatures exceeded 30 ˚C, while Durvillaea was exposed for up to 3 hours per day during low tide. Follow-up surveys showed that all bull kelps were eliminated from Pile Bay, and from all reefs within and immediately outside of Lyttelton Harbour. Following the localized extinction of bull kelp in Pile Bay, the invasive kelp Undaria pinnatifida recruited in high densities (average of 120 m-2). We conclude that bull kelps are likely to experience additional mortalities in the future because heatwaves are predicted to increase in magnitude and durations. Losses of the endemic D. poha are particularly concerning due to its narrow distributional range.