Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of Ex Vivo Expansion of Limbal Epithelial Progenitors by Maintaining Native Niche Cells on Denuded Amniotic Membrane.

PURPOSE Transplantation of ex vivo expanded limbal epithelial progenitor cells (LEPCs) on epithelially denuded amniotic membrane (dAM) in supplemented hormonal epithelial medium (SHEM) is an alternative solution for treating corneal blindness due to limbal stem cell (SC) deficiency. Because the phenotype of limbal niche cells (NCs) is preserved better in serum-free modified embryonic stem cell (ESC) medium (MESCM) than SHEM, we question whether the aforementioned expansion protocol can be further optimized by maintaining limbal NCs using MESCM. METHODS Collagenase-isolated limbal clusters were cultured on dAM in SHEM or MESCM for 8 to 10 days. Epithelial outgrowth sheets removed by dispase were subjected to real-time quantitative polymerase chain reaction (qPCR) and immunostaining for expression of corneal epithelial markers (p63α, pax6, and K12) and NC markers (FLK-1, CD34, CD31, PDGFR-B, and α-SMA). A total of 1000 single cells were seeded on 6-well dish containing 3T3 feeder layers for 12 to 14 days before rhodamine B staining. RESULTS Epithelial outgrowth in SHEM showed a significant loss of corneal SC and ESC markers when compared with freshly collagenase-isolated limbal clusters. Although the epithelial outgrowth was slower in MESCM, epithelial cell size was consistently smaller than that found in SHEM. Furthermore, MESCM maintained a significantly higher percentage of PCK-/ Vim+ cells and exhibited a significant upregulation of NC markers and corneal epithelial SC markers (K15, Bmi-1, and Msi-1) than SHEM. Furthermore, the number of purported holoclones was significantly promoted in MESCM than SHEM. CONCLUSION These data collectively suggest that MESCM can be used to replace SHEM to further promote expansion of LEPC by maintaining limbal native NCs. TRANSLATIONAL RELEVANCE Effective ex vivo expansion of limbal epithelial SC is a first and important step toward the success of treating corneal blindness caused by limbal stem cell deficiency and paves the way for future applications in regenerative medicine.
Crystallization and nanoindentation behavior of a bulk Zr–Al–Ti–Cu–Ni amorphous alloy

The crystallization and nanoindentation behavior of a Zr–10Al–5Ti–17.9Cu–14.6Ni (at.%) bulk amorphous alloy (BAA) were studied. Resulting from the kinetic nature of phase transformation in multicomponent alloys, the crystallization path is complex. Despite the complexity of different crystallization paths, the main final crystallized product in the Zr-based BAA is Zr_2Cu. Young’s modulus and hardness of the BAA were found to increase with an increase in annealing temperature. The observed mechanical properties were correlated with the microstructure of the material. Also, in the present paper, both the observed crystallization and nanoindentation behavior are compared with existing data. Zr-based BAAs exhibit a ratio of hardness to Young’s modulus (H/E ratio) of about 1/10, suggesting the interatomic bonding in the alloys is close to being covalent.
Predicting occurrence of juvenile shark habitat to improve conservation planning

Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark‐monitoring data on large scales (100s–1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of habitat suitability for juvenile sharks. We assessed occurrence patterns at the order and species levels. We included all juvenile sharks sampled and the 3 most abundant species sampled separately (grey reef [Carcharhinus amblyrhynchos], sandbar [Carcharhinus plumbeus], and whitetip reef sharks [Triaenodon obesus]). We predicted the occurrence of juvenile sharks across 490,515 km2 of coastal waters and quantified the representation of highly suitable habitats within MPAs. Our species‐level models had higher accuracy (ĸ ≥ 0.69) and deviance explained (≥48%) than our order‐level model (ĸ = 0.36 and deviance explained of 10%). Maps of predicted occurrence revealed different species‐specific patterns of highly suitable habitat. These differences likely reflect different physiological or resource requirements between individual species and validate concerns over the utility of conservation targets based on aggregate species groups as opposed to a species‐focused approach. Highly suitable habitats were poorly represented in MPAs with the most restrictions on extractive activities. This spatial mismatch possibly indicates a lack of explicit conservation targets and information on species distribution during the planning process. Non‐extractive BRUVS provided a useful platform for building the suitability models across large scales to assist conservation planning across multiple maritime jurisdictions, and our approach provides a simple for method for testing the effectiveness of MPAs.
Molecular Techniques for Identification of Species of the Mycobacterium tuberculosis Complex: The use of Multiplex PCR and an Adapted HPLC Method for Identification of Mycobacterium bovis and Diagnosis of Bovine Tuberculosis

Mycobacterium bovis is a member of the M. tuberculosis complex (MTC), a group of species (Mycobacterium tuberculosis, M. bovis, M. africanum, M. microti, and M. canetti) with a high genetic homology. M. bovis is the causative agent of tuberculosis in a range of animal species and humans, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette–Guérin vaccine strain, the most widely used human vaccine. Garnier et al. (2003) described the 4,345,492-bp genome sequence of M. bovis AF2122/97 and compared it with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has reduced the genome size.
A Group of 500 Women Whose Health May Depart Notably From the Norm: Protocol for a Cross-Sectional Survey

Background Longitudinal studies of women’s health often seek to identify predictors of good health. Research has shown that following simple guidelines can halve women’s mortality. The ongoing Australian Longitudinal Study of Women’s Health (ALSWH) shows that Australian women are getting better at reducing their smoking and alcohol use, and are generally diligent about attending recommended health screenings, but are becoming less successful at dealing with obesity. There are communities of women who live unusually healthy lives (Rosetans, Seventh-Day Adventists, traditional Japanese women), but their lifestyles are unlikely to be adopted widely. Universal Medicine (UM) is a complementary-to-medicine approach that emphasizes personal empowerment and the importance of menstrual health symptoms. Objective This survey investigates whether the approximately 500 women associated with UM exhibit health status significantly above the norm. As part of this investigation, questions for a newly developed menstrual attitudes questionnaire will also be evaluated. Methods A quantitative cross-sectional survey of women in a UM cohort was designed with the help of three focus groups of women at three life stages: in menses, peri-menopausal, and menopausal. The menstrual attitudes portion of the survey incorporates the insights of these women regarding female health issues. The survey also includes 41 questions taken from the ALSWH. Focus groups generated additional questions about symptoms experienced and attitudes toward female health issues. ALSWH questions, including a range of health scales like the Short Form 36 (SF-36), Center for Epidemiologic Studies Depression Scale, Perceived Control Scale, Kessler Psychological Distress Scale, and the Multi-Item Summed Score for Perceived Stress, along with questions about experienced major health events, were investigated and incorporated if considered suitable. At the time of publication of this protocol, data collection has been completed. Results The validity of the menstrual attitudes questionnaire will be evaluated with Cohen’s kappa. ALSWH respondents and UM participants will be compared, using unweighted regression or regression weighted or normalized by age, education, and interest in alternative treatments (to increase comparability), as appropriate. Analyses will determine whether UM-related variables (being a UM participant, length of UM participation, number of UM events attended) are associated with: differences in the number of major health events and health symptoms experienced; SF-36 physical and mental health scores; body mass index; and consumption of alcohol, tobacco, sugar, salt, caffeine, and dairy. Conclusions If women in the UM cohort are truly in substantially better health than the norm, further investigations may be worthwhile to see whether UM plays a causal role, and whether the women’s practices are generalizable. International Registered Report Identifier (IRRID) DERR1-10.2196/7993
MISO in Ultra-Dense Networks: Balancing the Tradeoff between User and System Performance

With over-deployed network infrastructures, network densification is shown to hinder the improvement of user experience and system performance. In this paper, we adopt multi-antenna techniques to overcome the bottleneck and investigate the performance of single-user beamforming, an effective method to enhance desired signal power, in small cell networks from the perspective of user coverage probability (CP) and network spatial throughput (ST). Pessimistically, it is proved that, even when multi-antenna techniques are applied, both CP and ST would be degraded and even asymptotically diminish to zero with the increasing base station (BS) density. Moreover, the results also reveal that the increase of ST is at the expense of the degradation of CP. Therefore, to balance the tradeoff between user and system performance, we further study the critical density, under which ST could be maximized under the CP constraint. Accordingly, the impact of key system parameters on critical density is quantified via the derived closed-form expression. Especially, the critical density is shown to be inversely proportional to the square of antenna height difference between BSs and users. Meanwhile, single-user beamforming, albeit incapable of improving CP and ST scaling laws, is shown to significantly increase the critical density, compared to the single-antenna regime.
Suitability of Monotypic and Mixed Diets for Anopheles hermsi Larval Development

ABSTRACT: The developmental time and survival to eclosion of Anopheles hermsi Barr & Guptavanij fed monotypic and mixed diets of ten food types were examined in laboratory studies. Larvae fed monotypic diets containing animal detritus (freeze-dried rotifers, freeze-dried Daphnia pulicaria, and TetraMin® fish food flakes) and the mixotrophic protistan Cryptomonas ovata developed faster and survived better than larvae that were fed other monotypic diets. Survival to adulthood of larvae fed several concentrations of the diatom Planothidium (=Achnanthes) lanceolatum was poor (<13%) and larval development time was approximately twice that of larvae fed TetraMin® fish food flakes, the standard laboratory diet. Larvae fed monotypic diets containing prokaryotes (bacteria [Bacillus cereus] and cyanobacteria [Oscillatoria prolifera]) and brewer's yeast (Saccharomyces cerevisiae) failed to survive beyond the 1st and 2nd instar, respectively. Larvae fed only chlorophytes, single-celled Chlamydomonas reinhardtii and filamentous Spirogyra communis, failed to complete larval development, regardless of the concentration tested. Cohorts fed a combination of food types (mixed diets) usually developed better than cohorts fed monotypic diets. Food types that failed to support complete development when fed alone often facilitated development to adulthood when fed in combination with food types containing >1% C20 polyunsaturated fatty acids as total fat, but regardless of essential fatty acid content, algae that produced mucilage and filaments that sank out of the feeding zone were poor quality diets.
Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex

ABSTRACT All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.
Assessment of hysteroscopic role in management of women with recurrent pregnancy loss

Abstract Objectives: To assess the hysteroscopic value in the management of intrauterine lesion in women with recurrent pregnancy loss. Methods: This study was done in Ain Shams Maternity Hospital after the approval of the research Ethics Committee, during the period between August 2014 and December 2015 where 200 nonpregnant women with a history of three or more consecutive unexplained first and second trimester miscarriages before 20 weeks were recruited from recurrent miscarriage clinic. A written informed consent was obtained from all women before participation. Results: This current study was conducted in Ain Shams University Maternity Hospital during the period between August 2014 to May 2015 a total of 200 women with history of recurrent miscarriage were included in the study. Regarding the results of this study the mean age was 30.5(5.7), the mean number of previous abortion 3(3–5) the mean number of the first trimesteric abortion was 2 with range (2–2) the mean number of second trimesteric abortion was 2 with range (1–2). In this study, 88% of patients were nullipara. It was also found that hysteroscopic findings were found in 58.5%. Uterine anomalies was present in 21%, including septate uterus and intrauterine adhesion (IUAs) were present in 12.5%. Endometrial polyps were present in 8.5%, bicornute uterus in 4.5%, unicornuate uterus in 4.5% while submucous myomas were present in 7.5%. It was found that 48.5% need hysteroscopic intervention including 21% need septectomy 12.5% need adhesiolysis, 6.5% need myomectomy while 8.5% need polypectomy. The study found that no statistically significant difference between patients with normal hysteroscopic finding and patients with abnormal hysteroscopic finding as regard age, time of previous abortion and number of previous abortion. But there was statistically significant difference as regard number of previous delivery and abnormal HSG. Conclusions: It appears that hysteroscopy is a useful tool in the diagnosis and treatment of the causes of recurrent miscarriage that can be performed safely without anesthesia in most cases. The prevalence of uterine anomalies in patients with recurrent miscarriages is 54.5%, septate uterus is the most common anomaly and for this reason uterine anomalies should be systematically assessed in patients with recurrent miscarriage.
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text

Abstract Motivation Best performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models. Results We propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems. Availability and implementation The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN. Supplementary information Supplementary data are available at Bioinformatics online.
Both Paraoxonase-1 Genotype and Activity Do Not Predict the Risk of Future Coronary Artery Disease; the EPIC-Norfolk Prospective Population Study

BACKGROUND Paraoxonase-1 (PON1) is an antioxidant enzyme, that resides on high-density lipoprotein (HDL). PON1-activity, is heavily influenced by the PON1-Q192R polymorphism. PON1 is considered to protect against atherosclerosis, but it is unclear whether this relation is independent of its carrier, HDL. In order to evaluate the atheroprotective potential of PON1, we assessed the relationships among PON1-genotype, PON1-activity and risk of future coronary artery disease (CAD), in a large prospective case-control study. METHODOLOGY/PRINCIPAL FINDINGS Cases (n = 1138) were apparently healthy men and women aged 45-79 years who developed fatal or nonfatal CAD during a mean follow-up of 6 years. Controls (n = 2237) were matched by age, sex and enrollment time. PON1-activity was similar in cases and controls (60.7+/-45.3 versus 62.6+/-45.8 U/L, p = 0.3) and correlated with HDL-cholesterol levels (r = 0.16, p<0.0001). The PON1-Q192R polymorphism had a profound impact on PON1-activity, but did not predict CAD risk (Odds Ratio [OR] per R allele 0.98[0.84-1.15], p = 0.8). Using conditional logistic regression, quartiles of PON1-activity showed a modest inverse relation with CAD risk (OR for the highest versus the lowest quartile 0.77[0.63-0.95], p = 0.01; p-trend = 0.06). PON1-activity adjusted for Q192R polymorphism correlated better with HDL-cholesterol (r = 0.26, p<0.0001) and more linearly predicted CAD risk (0.79[0.64-0.98], p = 0.03; p-trend = 0.008). However, these relationships were abolished after adjustment for HDL (particles-cholesterol-size) and apolipoproteinA-I (0.94[0.74-1.18], p-trend = 0.3). CONCLUSIONS/SIGNIFICANCE This study, shows that PON1-activity inversely relates to CAD risk, but not independent of HDL, due to its close association with the HDL-particle. These data strongly suggest that a low PON1-activity is not a causal factor in atherogenesis.
A Comprehensive Approach to the Recognition, Diagnosis, and Severity‐Based Treatment of Focal Hyperhidrosis: Recommendations of the Canadian Hyperhidrosis Advisory Committee

BACKGROUND Hyperhidrosis can have profound effects on a patient's quality of life. Current treatment guidelines ignore disease severity. OBJECTIVE The objective was to establish clinical guidelines for the recognition, diagnosis, and treatment of primary focal hyperhidrosis. METHODS AND MATERIALS A working group of eight nationally recognized experts was convened to develop the consensus statement using an evidence-based approach. RECOMMENDATIONS An algorithm was designed to consider both disease severity and location. The Hyperhidrosis Disease Severity Scale (HDSS) provides a qualitative measure that allows tailoring of treatment. Mild axillary, palmar, and plantar hyperhidrosis (HDSS score of 2) should initially be treated with topical aluminum chloride (AC). If the patient fails to respond to AC therapy, botulinum toxin A (BTX-A; axillae, palms, soles) and iontophoresis (palms, soles) should be the second-line therapy. In severe cases of axillary, palmar, and plantar hyperhidrosis (HDSS score of 3 or 4), both BTX-A and topical AC are first-line therapy. Iontophoresis is also first-line therapy for palmar and plantar hyperhidrosis. Craniofacial hyperhidrosis should be treated with oral medications, BTX-A, or topical AC as first-line therapy. Local surgery (axillary) and endoscopic thoracic sympathectomy (palms and soles) should only be considered after failure of all other treatment options. CONCLUSIONS These guidelines offer a rapid method to assess disease severity and to treat primary focal hyperhidrosis according to severity.
Empirically Derived Dietary Patterns in UK Adults Are Associated with Sociodemographic Characteristics, Lifestyle, and Diet Quality

The aim of this study was to examine empirical dietary patterns in UK adults and their association with sociodemographic characteristics, lifestyle factors, self-reported nutrient intake, nutrient biomarkers, and the Nutrient-based Diet Quality Score (NDQS) using National Diet and Nutrition Survey data 2008–2012 (n = 2083; mean age 49 years; 43.3% male). Four patterns explained 13.6% of the total variance: ‘Snacks, fast food, fizzy drinks’ (SFFFD), ‘Fruit, vegetables, oily fish’ (FVOF), ‘Meat, potatoes, beer’ (MPB), and ‘Sugary foods, dairy’ (SFD). ‘SFFFD’ was associated positively with: being male; smoking; body mass index (BMI); urinary sodium; intake of non-milk extrinsic sugars (NMES), fat and starch; and negatively with: age; plasma carotenoids; and NDQS. ‘FVOF’ was associated positively with: being non-white; age; income; socioeconomic classification (National Statistics Socio-economic Classifications; NSSEC); plasma carotenoids; intake of non-starch polysaccharides and polyunsaturated fatty acids. It was negatively associated with: being male, smoking, BMI, urinary sodium, intake of saturated fat; and NMES and NDQS. Whilst the patterns explained only 13.6% of the total variance, they were associated with self-reported nutrient intake, biomarkers of nutrient intake, sociodemographic and lifestyle variables, and the NDQS. These findings provide support for dietary patterns analyses as a means of exploring dietary intake in the UK population to inform public health nutrition policy and guidance.