Miracle-dz/UniFAR-FTUs huggingface dataset:
Amphibian responses to livestock use of wetlands: new empirical data and a global review.

Pastureland currently occupies 26% of Earth's ice-free land surface. As the global human population continues to increase and developing countries consume more protein-rich diets, the amount of land devoted to livestock grazing will only continue to rise. To mitigate the loss of global biodiversity as a consequence of the ever-expanding amount of land converted from native habitat into pastureland for livestock grazing, an understanding of how livestock impact wildlife is critical. While previous reviews have examined the impact of livestock on a wide variety of taxa, there have been no reviews examining how global livestock grazing affects amphibians. We conducted both an empirical study in south-central Florida examining the impact of cattle on amphibian communities and a quantitative literature review of similar studies on five continents. Our empirical study analyzed amphibian community responses to cattle as both a binary (presence/absence) variable, and as a continuous variable based on cow pie density. Across all analyses, we were unable to find any evidence that cattle affected the amphibian community at our study site. The literature review returned 46 papers that met our criteria for inclusion. Of these studies, 15 found positive effects of livestock on amphibians, 21 found neutral/mixed effects, and 10 found negative effects. Our quantitative analysis of these data indicates that amphibian species that historically occurred in closed-canopy habitats are generally negatively affected by livestock presence. In contrast, open-canopy amphibians are likely to experience positive effects from the presence of livestock, and these positive effects are most likely to occur in locations with cooler climates and/or greater precipitation seasonality. Collectively, our empirical work and literature review demonstrate that under the correct conditions well-managed rangelands are able to support diverse assemblages of amphibians. These rangeland ecosystems may play a critical role in protecting future amphibian biodiversity by serving as an "off-reserve" system to supplement the biodiversity conserved within traditional protected areas. This article is protected by copyright. All rights reserved.
Longitudinal change of sleep timing: association between chronotype and longevity in older adults

ABSTRACT Evening-oriented sleep timing preferences have been associated with risk of diabetes, cardiovascular diseases, obesity, psychiatric disorders, and increased mortality. This research aims to explore the relationship between diurnal preferences (chronotype), daily habits, metabolic health, and mortality, using longitudinal data from The University of Manchester Longitudinal Study of Cognition in Normal Healthy Old Age (6375 participants at inception, recruited in the North of England) with a long follow-up period (up to 35.5 years). Mixed models were used to investigate the influence of aging, socio-demographic, and seasonal factors on sleep timing. Results show that sleep timing shifted towards earlier time with aging. Test seasons influence chronotype of older adults but working schedules challenge seasonality of sleep timing. Moreover, the season of birth may set chronotype in adulthood. Individual chronotype trajectories were clustered using latent class analysis and analyzed against metabolic health and mortality. We observed a higher risk of hypertension in the evening-type cluster compared to morning-type individuals (Odds ratio = 1.88, 95%CI = 1.02/3.47, p = .04). Evening-type cluster was also associated with traits related to lower health such as reduced sport participation, increased risk of depression and psychoticism personality, late eating, and increased smoking and alcohol usage. Finally, Cox regression of proportional hazards was used to study the effects of chronotype on longevity after adjusting for sleep duration, age, gender, smoking, alcohol usage, general health, and social class. The survival analysis (82.6% censored by death) revealed that evening-type chronotype increased the likelihood of mortality (Hazard ratio = 1.15, 95%CI = 1.04/1.26, p = .005). Taken together, chronotype is influenced by aging and seasonal effects. Evening-type preference may have detrimental outcomes for human well-being and longevity.
Are acceleration and cardiovascular capacities related to perceived load in professional soccer players?

ABSTRACT This study aims at assessing physical fitness performance and its relationship with the differential ratings of perceived exertion of training load (dRPE TL) and match load (dRPE ML) in a Spanish professional soccer team at the beginning of several in-season periods: 1–4 weeks, 5–8 weeks and 1–8 weeks. Performance and mechanical variables over the acceleration phase, as well as cardiovascular performance variables were evaluated in 20 male professional soccer players of a team competing in the Spanish Second Division League. Moreover, dRPE TL and dRPE ML were quantified. The dRPE TL showed negative and large associations between both maximal aerobic speed (MAS) and maximal oxygen consumption (VO2max) (from r = −0.53; ± 0.06 to r = −0.53; ± 0.05 95% CL, p = 0.035 to 0.036) and RPEres TL values throughout the 5–8 and 1–8 week periods. Furthermore, dRPE ML positive and large associations were found between players initial MAS or VO2max (from r = 0.50; ± 0.17 to r = 0.56; ± 0.11 95% CL, p = 0.026 to 0.049) and RPEmus ML in 1–4 and 1–8 week periods. The current study suggests that a better cardiovascular capacity could be connected with a lower RPEres TL and higher RPEmus ML.
High Functioning Autism with Missense Mutations in Synaptotagmin-Like Protein 4 (SYTL4) and Transmembrane Protein 187 (TMEM187) Genes: SYTL4- Protein Modeling, Protein-Protein Interaction, Expression Profiling and MicroRNA Studies

We describe a 7-year-old male with high functioning autism spectrum disorder (ASD) and maternally-inherited rare missense variant of Synaptotagmin-like protein 4 (SYTL4) gene (Xq22.1; c.835C>T; p.Arg279Cys) and an unknown missense variant of Transmembrane protein 187 (TMEM187) gene (Xq28; c.708G>T; p. Gln236His). Multiple in-silico predictions described in our study indicate a potentially damaging status for both X-linked genes. Analysis of predicted atomic threading models of the mutant and the native SYTL4 proteins suggest a potential structural change induced by the R279C variant which eliminates the stabilizing Arg279-Asp60 salt bridge in the N-terminal half of the SYTL4, affecting the functionality of the protein’s critical RAB-Binding Domain. In the European (Non-Finnish) population, the allele frequency for this variant is 0.00042. The SYTL4 gene is known to directly interact with several members of the RAB family of genes, such as, RAB27A, RAB27B, RAB8A, and RAB3A which are known autism spectrum disorder genes. The SYTL4 gene also directly interacts with three known autism genes: STX1A, SNAP25 and STXBP1. Through a literature-based analytical approach, we identified three of five (60%) autism-associated serum microRNAs (miRs) with high predictive power among the total of 298 mouse Sytl4 associated/predicted microRNA interactions. Five of 13 (38%) miRs were differentially expressed in serum from ASD individuals which were predicted to interact with the mouse equivalent Sytl4 gene. TMEM187 gene, like SYTL4, is a protein-coding gene that belongs to a group of genes which host microRNA genes in their introns or exons. The novel Q236H amino acid variant in the TMEM187 in our patient is near the terminal end region of the protein which is represented by multiple sequence alignments and hidden Markov models, preventing comparative structural analysis of the variant harboring region. Like SYTL4, the TMEM187 gene is expressed in the brain and interacts with four known ASD genes, namely, HCFC1; TMLHE; MECP2; and GPHN. TMM187 is in linkage with MECP2, which is a well-known determinant of brain structure and size and is a well-known autism gene. Other members of the TMEM gene family, TMEM132E and TMEM132D genes are associated with bipolar and panic disorders, respectively, while TMEM231 is a known syndromic autism gene. Together, TMEM187 and SYTL4 genes directly interact with recognized important ASD genes, and their mRNAs are found in extracellular vesicles in the nervous system and stimulate target cells to translate into active protein. Our evidence shows that both these genes should be considered as candidate genes for autism. Additional biological testing is warranted to further determine the pathogenicity of these gene variants in the causation of autism.
Role of a Contactin multi‐molecular complex secreted by oligodendrocytes in nodal protein clustering in the CNS

The fast and reliable propagation of action potentials along myelinated fibers relies on the clustering of voltage‐gated sodium channels at nodes of Ranvier. Axo‐glial communication is required for assembly of nodal proteins in the central nervous system, yet the underlying mechanisms remain poorly understood. Oligodendrocytes are known to support node of Ranvier assembly through paranodal junction formation. In addition, the formation of early nodal protein clusters (or prenodes) along axons prior to myelination has been reported, and can be induced by oligodendrocyte conditioned medium (OCM). Our recent work on cultured hippocampal neurons showed that OCM‐induced prenodes are associated with an increased conduction velocity (Freeman et al., 2015). We here unravel the nature of the oligodendroglial secreted factors. Mass spectrometry analysis of OCM identified several candidate proteins (i.e., Contactin‐1, ChL1, NrCAM, Noelin2, RPTP/Phosphacan, and Tenascin‐R). We show that Contactin‐1 combined with RPTP/Phosphacan or Tenascin‐R induces clusters of nodal proteins along hippocampal GABAergic axons. Furthermore, Contactin‐1‐immunodepleted OCM or OCM from Cntn1‐null mice display significantly reduced clustering activity, that is restored by addition of soluble Contactin‐1. Altogether, our results identify Contactin‐1 secreted by oligodendrocytes as a novel factor that may influence early steps of nodal sodium channel cluster formation along specific axon populations.
Hyperspectral Spectrometry as a Means to Differentiate Uninfested and Infested Winter Wheat by Greenbug (Hemiptera: Aphididae)

Abstract Although spectral remote sensing techniques have been used to study many ecological variables and biotic and abiotic stresses to agricultural crops over decades, the potential use of these techniques for greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae) infestations and damage to wheat, Triticum aestivum L. , under field conditions is unknown. Hence, this research was conducted to investigate: 1) the applicability and feasibility of using a portable narrow-banded (hyperspectral) remote sensing instrument to identify and discern differences in spectral reflection patterns (spectral signatures) of winter wheat canopies with and without greenbug damage; and 2) the relationship between miscellaneous spectral vegetation indices and greenbug density in wheat canopies growing in two fields and under greenhouse conditions. Both greenbug and reflectance data were collected from 0.25-, 0.37-, and 1-m2 plots in one of the fields, greenhouse, and the other field, respectively. Regardless of the growth conditions, greenbug-damaged wheat canopies had higher reflectance in the visible range and less in the near infrared regions of the spectrum when compared with undamaged canopies. In addition to percentage of reflectance comparison, a large number of spectral vegetation indices drawn from the literature were calculated and correlated with greenbug density. Linear regression analyses revealed high relationships (R2 ranged from 0.62 to 0.85) between greenbug density and spectral vegetation indices. These results indicate that hyperspectral remotely sensed data with an appropriate pixel size have the potential to portray greenbug density and discriminate its damage to wheat with repeated accuracy and precision.
Identification of human herpes virus 1 encoded microRNAs in biopsy samples of lower esophageal sphincter muscle during peroral endoscopic myotomy for esophageal achalasia

Esophageal achalasia is a rare chronic debilitating disorder characterized by incomplete lower esophageal sphincter (LES) relaxation and abnormal peristalsis as a result of myenteric plexus degeneration. Although complex interactions among immunity, viruses and inheritance have been proposed, its causes remain unknown. MicroRNAs (miRs) play crucial roles in the regulation of gene expression during pathophysiological processes. Certain viruses such as herpes simplex virus (HSV) encode miRs derived from their own genomes. To determine the underlying relationship of miRNAs to achalasia, we analyzed the expression profile of miRNAs using biopsy samples obtained from LES muscle during peroral endoscopic myotomy. Peroral LES muscle biopsy sampling was uneventfully carried out in our case series of achalasia. Control biopsy tissues were also obtained from LES muscle of patients without symptoms relating to abnormal esophageal motility whose esophagogastric junction was surgically excised. RNA was extracted from biopsy specimens and analyzed using a microarray. Differentially expressed miRNAs in achalasia patients compared to controls were identified and analyzed using reverse transcription quantitative polymerase chain reaction. HSV‐1‐derived hsv1‐miR‐H1 and ‐H18 was significantly overexpressed in achalasia cohorts compared to controls. Correlations between the expression levels of viral miR and the patients’ clinical characteristics including achalasia morphological type, dilatation grading, and disease duration were not identified. Further studies with a larger sample size are needed to replicate the current heuristic identification of neurotropic viral miRs and unravel their functional significance in order to provide new insight linking neurodegenerative etiology in achalasia.
Influence of Equimolar Doses of Beetroot Juice and Sodium Nitrate on Time Trial Performance in Handcycling

This study aimed to investigate the influence of a single dose of either beetroot juice (BR) or sodium nitrate (NIT) on performance in a 10 km handcycling time trial (TT) in able-bodied individuals and paracyclists. In total, 14 able-bodied individuals [mean ± SD; age: 28 ± 7 years, height: 183 ± 5 cm, body mass (BM): 82 ± 9 kg, peak oxygen consumption (VO2peak): 33.9 ± 4.2 mL/min/kg] and eight paracyclists (age: 40 ± 11 years, height: 176 ± 9cm, BM: 65 ± 9 kg, VO2peak: 38.6 ± 10.5 mL/min/kg) participated in the study. All participants had to perform three TT on different days, receiving either 6 mmol nitrate as BR or NIT or water as a placebo. Time-to-complete the TT, power output (PO), as well as oxygen uptake (VO2) were measured. No significant differences in time-to-complete the TT were found between the three interventions in able-bodied individuals (p = 0.80) or in paracyclists (p = 0.61). Furthermore, VO2 was not significantly changed after the ingestion of BR or NIT in either group (p < 0.05). The PO to VO2 ratio was significantly higher in some kilometers of the TT in able-bodied individuals (p < 0.05). The ingestion of BR or NIT did not increase handcycling performance in able-bodied individuals or in paracyclists.
Predictors of Multidrug-Resistant Tuberculosis (MDR-TB) in Sudan

Multidrug-resistant tuberculosis (MDR-TB) is a global public health threat and burden on the health system. This is especially the case in high tuberculosis (TB) prevalence countries, such as Sudan. Consequently, this study aimed to ascertain the predictors of MDR-TB in Sudan to provide future guidance. An unmatched case-control study to assess the predictors of MDR-TB infections among the Sudanese population was conducted from August 2017 to January 2018 at Abu-Anga referral hospital. Patients’ data was gathered from patients’ cards and via interviews. A structured pre-validated questionnaire was used to gather pertinent information, which included sociodemographic characteristics and other relevant clinical data. Univariate and multivariate logistic regression analysis was employed to determine the predictors of MDR-TB infection. 76 of the 183 patients interviewed (41.5%) had MDR-TB cases. The independent predictors for MDR-TB were living in rural areas [adjusted odds ratio (aOR) = 3.1 (95% confidence interval (CI): 1.2–8.2)], treatment failure [aOR = 56.9 (10.2–319.2)], and smoking [(aOR = 4 (1.2–13.2)], whereas other sociodemographic factors did not predict MDR-TB. In conclusion, the study showed that a history of smoking, living in rural areas, and a previous treatment failure were the predictors of MDR-TB in Sudan. The latter factors are most likely due to issues that are related to access and adherence to treatment and lifestyle. The existence of any of these factors among newly diagnosed TB patients should alert clinicians for the screening of MDR-TB. The implementation of directly observed treatment (DOT) and health education are crucial in stopping the spread of MDR-TB in Sudan.
Nephromyces Represents a Diverse and Novel Lineage of the Apicomplexa That Has Retained Apicoplasts

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to 1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, 2) search for the apicoplast genome of Nephromyces, and 3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the nonphotosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.
Generation of Amelx-iCre Mice Supports Ameloblast-Specific Role for Stim1

The identification and targeting of the molecular pathways regulating amelogenesis is an ongoing challenge in dental research, and progress has been restricted by the limited number of genetic tools available to study gene function in ameloblasts. Here, we generated 4 transgenic Cre-driver mouse lines that express improved Cre (iCre)–recombinase from the locus of the mouse ameloblast-specific gene amelogenin X (Amelx-iCre) with a large (250-kb) bacterial artificial chromosome DNA vector. All 4 Amelx-iCre transgenic lines were bred with ROSA26 reporter mice to characterize the iCre developmental pattern with the LacZ gene encoding β-galactosidase enzyme activity assay and Cre protein immunohistochemistry. From the 4 generated transgenic lines, 2 were selected for further analysis because they expressed a high amount of Cre recombinase exclusively in ameloblasts and showed developmental stage- and cell-specific β-galactosidase activity mimicking the endogenous amelogenin expression. To test the functionality of the selected transgenic models, we bred the 2 Amelx-iCre mice lines with stromal interaction molecule 1 (Stim1) floxed mice to generate ameloblast-specific Stim1 conditional knockout mice (Stim1 cKO). STIM1 protein serves as one of the main calcium sensors in ameloblasts and plays a major role in enamel mineralization and ameloblast differentiation. Amelx-iCre mice displayed exclusive CRE-mediated recombination in incisor and molar ameloblasts. Stim1 cKO mice showed a severely defected enamel phenotype, including reduced structural integrity concomitant with increased attrition and smaller teeth. The phenotype and genotype of the Amelx-iCre/Stim1 cKO showed significant differences with the previously reported Ker14-Cre/Stim1 cKO, highlighting the need for cell- and stage-specific Cre lines for an accurate phenotype-genotype comparison. Furthermore, our model has the advantage of carrying the entire Amelx gene locus rather than being limited to an Amelx partial promoter construct, which greatly enhances the stability and the specificity of our Cre expression. As such, the Amelx-iCre transgenic lines that we developed may serve as a powerful tool for targeting ameloblast-specific gene expression in future investigations.
Do, say, learn: the functions of mothers’ speech to infants

Abstract We examined the functions of mothers’ speech to infants during two tasks – book-sharing and bead-stringing – in low-income, ethnically diverse families. Mexican, Dominican, and African American mothers and their infants were video-recorded sharing wordless books and toy beads in the home when infants were aged 1;2 and 2;0. Mothers’ utterances were classified into seven categories (labels/descriptions, emotion/state language, attention directives, action directives, prohibitions, questions, and vocal elicitations) which were grouped into three broad language functions: referential language, regulatory language, and vocalization prompts. Mothers’ ethnicity, years of education, years living in the United States, and infant sex and age related to mothers’ language functions. Dominican and Mexican mothers were more likely to use regulatory language than were African American mothers, and African American mothers were more likely to use vocalization prompts than were Latina mothers. Vocalization prompts and referential language increased with mothers’ education and Latina mothers’ years living in the United States. Finally, mothers of boys used more regulatory language than did mothers of girls. Socio-cultural and developmental contexts shape the pragmatics of mothers’ language to infants.
Rare Mesenteric Arterial Diseases: Fibromuscular Dysplasia and Segmental Arterial Mediolysis and Literature Review

Fibromuscular dysplasia (FMD) and segmental arterial mediolysis (SAM) are noninflammatory, nonatherosclerotic arterial diseases that cause aneurysm, occlusion, and thromboses. These diseases are rarely seen in mesenteric arterial lesions; however, as they can be lethal if appropriate management is not provided, the accumulation of clinical information from cases is essential. We herein report the cases of a 57-year-old man diagnosed with FMD and a 63-year-old man diagnosed with SAM. We conclude that an early diagnosis with imaging modalities and clinical information followed by the appropriate treatment improves the prognosis of these arterial diseases.