Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomy of the Sylvilagus brasiliensis complex in Central and South America (Lagomorpha: Leporidae)

A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that—absent any type material—S. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus.
Factors associated with difficulty in using the community based services among children with special health care needs

Sreelakshmi Talasila, Factors Associated with Difficulty in using the Community Based Services Among Children with Special Health Care Needs. Master of Public Health (Biostatistics), December 2009, 73 pp, 5 tables, 1 illustration, bibliography, 36 titles. Despite various advances in the health care system, children with special health care needs (CSHCN) face difficulty in accessing required services. The purpose of this study was to identify factors associated with difficulty in using community based services, individual barriers and institutional barriers for CSHCN. Data were obtained from National Survey of CSHCN 2005-06. The Andersen Health Behavioral Model was used to identify predisposing, enabling and need factors. Logistic regression was performed. Education, region, race/ethnicity, number of children, insurance and satisfaction with services were associated with community based services. Results suggest functional limitations and severity of illness are associated with difficulty in using community based services. Further investigation is required to improve health care system.
A new species concept for the clinically relevant Mucor circinelloides complex

Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides complex – MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus.
The Evolution of Early Vascular Plant Complexity

Premise of research. The concept of biological complexity is deeply embedded in evolutionary theory and empirical enquiry. Yet it is largely used intuitively and rarely quantified. Here, building on a previous phylogenetic analysis of 36 early Paleozoic tracheophytes and the extant genus Equisetum, we discuss the evolution of character states based on the consensus tree topology and the first appearance of derived character states in the fossil record in a preliminary attempt to quantify the tempo and mode of the evolution of complexity during a critical evolutionary period in land plant history. Methodology. Thirty-seven fossil taxa were selected (predominantly from the Silurian–Devonian time interval) to provide as many characters and character states as possible for each taxon to reduce the negative effects of missing characters in phylogenetic analyses and to most accurately represent phenotypic diversity. In addition, the character states of the extant taxon Equisetum were added to evaluate the phylogenetic position of this genus and its effect on the consensus tree. Pivotal results. Using the best-preserved taxa representative of their respective lineages, the consensus tree juxtaposed with the first recorded appearance of each fossil taxon showed that anatomical, morphological, and reproductive complexity increased throughout the time interval examined in this study and that this trend was attended by increasing body size within a well-defined zosterophyllophyte-lycophyte clade and a well-defined trimerophyte-euphyllophyte clade, distal to a rhyniophyte clade. Conclusions. The data indicate that (1) the taxa sampled segregate into two major tracheophyte “mega” clades (i.e., a trimerophyte-euphyllophyte clade and a zosterophyllophyte-lycophyte clade), (2) complexity (defined on the basis of four criteria and computed on the basis of the first occurrence of derived character states in the fossil record) and body size increased within each of the two mega clades, albeit at different tempi, and (3) substantial evolutionary convergence occurred (e.g., leaves, vascular cambia, roots, and aggregated reproductive structures).
Evidence for pre-climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.)

European pears (Pyrus communis L.) require a range of cold-temperature exposure to induce ethylene biosynthesis and fruit ripening. Physiological and hormonal responses to cold temperature storage in pear have been well characterized, but the molecular underpinnings of these phenomena remain unclear. An established low-temperature conditioning model was used to induce ripening of ‘D’Anjou’ and ‘Bartlett’ pear cultivars and quantify the expression of key genes representing ripening-related metabolic pathways in comparison to non-conditioned fruit. Physiological indicators of pear ripening were recorded, and fruit peel tissue sampled in parallel, during the cold-conditioning and ripening time-course experiment to correlate gene expression to ontogeny. Two complementary approaches, Nonparametric Multi-Dimensional Scaling and efficiency-corrected 2-(ΔΔCt), were used to identify genes exhibiting the most variability in expression. Interestingly, the enhanced alternative oxidase (AOX) transcript abundance at the pre-climacteric stage in ‘Bartlett’ and ‘D’Anjou’ at the peak of the conditioning treatments suggests that AOX may play a key and a novel role in the achievement of ripening competency. There were indications that cold-sensing and signaling elements from ABA and auxin pathways modulate the S1-S2 ethylene transition in European pears, and that the S1-S2 ethylene biosynthesis transition is more pronounced in ‘Bartlett’ as compared to ‘D’Anjou’ pear. This information has implications in preventing post-harvest losses of this important crop.
Genomic Variability and Recombination Analysis of Grapevine leafroll-associated virus-1 Isolates from Turkey

Asma yaprak kivirciklik virusu -1 (Grapevine leafroll-associated virus 1- GLRaV-1), asma yaprak kivirciklik hastaligina (Grapevine leafroll disease-GLRD) neden olan etmenler arasinda yer almakta olup dunya capinda virus kokenli bag hastaliklari arasinda onem derecesi yuksektir. Bu calismada, Turkiye’den izole edilen GLRaV-1’ in yayginlik derecesi, genetik varyasyonu ve rekombinasyon olaylari arastirilmistir. Ilk olarak, farkli bolgelerden toplanan 197 adet asma ornegi serolojik olarak test edilmistir. Test edilen orneklerden 109 adetinin (%55.32) GLRaV-1 ile infekte oldugu tespit edilmistir. Infekte oldugu tespit edilen bu ornekler arasindan her bir cografik bolgeyi temsil eden 9 adet izolat secilerek GLRaV-1’in kilif proteini (CP), ikincil kilif proteini (CPd2), acik okuma cercevesi 9 (p24) ve isi sok protein homologu 70 (HSP70h) gen bolgelerinin genetik analizleri yapilmistir. Yapilan analizlerde, calisilan dort gen bolgesinden CPd2 gen bolgesinin genetik cesitliliginin en yuksek oldugu gozlenirken en korumali bolgenin HSP70h geni oldugu tespit edilmistir. Gen Bankasindan alinan kayitlarin da kullanilmasi ile olusturulan filogenetik analizler sonucunda, izolatlarin iki buyuk grup altinda kumelendigi ve Turk izolatlarinin da cogunlukla ayni grup icerisinnde kumelendigi tespit edilmistir. Fakat, degisik cografik bolgelerden toplanan izolatlarin cografik bolgeye gore kumelenmedigi tespit edilmistir. Bununla birlikte, Rekombinasyon Bulma Programinda (RDP) yer alan algoritmalarin araciligi ile yapilan analizlerde cesitli rekombinasyon olaylari gozlenmistir. Sonuc olarak, elde edilen bu veriler GLRaV-1’in gerek ulkesel gerekse dunya capinda genetik varyasyon calismalarina katki saglamakta olup bagcilikta uretim materyallerinin sanitasyon programlarinin gelistirilmesine yardimci olacagi dusunulmektedir.
Polymorphisms in the Mitochondrial Genome Are Associated With Bullous Pemphigoid in Germans

Bullous pemphigoid (BP) is the most prevalent autoimmune skin blistering disease and is characterized by the generation of autoantibodies against the hemidesmosomal proteins BP180 (type XVII collagen) and BP230. Most intriguingly, BP is distinct from other autoimmune diseases because it predominantly affects elderly individuals above the age of 75 years, raising the question why autoantibodies and the clinical lesions of BP emerges mostly in this later stage of life, even in individuals harboring known putative BP-associated germline gene variants. The mitochondrial genome (mtDNA) is a potential candidate to provide additional insights into the BP etiology; however, the mtDNA has not been extensively explored to date. Therefore, we sequenced the whole mtDNA of German BP patients (n = 180) and age- and sex-matched healthy controls (n = 188) using next generation sequencing (NGS) technology, followed by the replication study using Sanger sequencing of an additional independent BP (n = 89) and control cohort (n = 104). While the BP and control groups showed comparable mitochondrial haplogroup distributions, the haplogroup T exhibited a tendency of higher frequency in BP patients suffering from neurodegenerative diseases (ND) compared to BP patients without ND (50%; 3 in 6 BP with haplogroup T). A total of four single nucleotide polymorphisms (SNPs) in the mtDNA, namely, m.16263T>C, m.16051A>G, and m.16162A>G in the D-loop region of the mtDNA, and m.11914G>A in the mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 gene (MT-ND4), were found to be significantly associated with BP based on the meta-analysis of our NGS data and the Sanger sequencing data (p = 0.0017, p = 0.0129, p = 0.0076, and p = 0.0132, respectively, Peto's test). More specifically, the three SNPs in the D-loop region were negatively, and the SNP in the MT-ND4 gene was positively associated with BP. Our study is the first to interrogate the whole mtDNA in BP patients and controls and to implicate multiple novel mtDNA variants in disease susceptibility. Studies using larger cohorts and more diverse populations are warranted to explore the functional consequences of the mtDNA variants identified in this study on immune and skin cells to understand their contributions to BP pathology.
Intra-operative pressure sores

As the extent of the pressure sore problem within hospitalized populations has been realized, their costs estimated and changes in the management of the NHS occurred, interest in pressure sores has increased and focused toward prevention. Research has served to underline the complexities of the issues involved and it is now acknowledged that the development of a pressure sore is dependent upon a complicated interplay of many variables, including the intensity and duration of pressure and the tolerance of the skin. The focus of this study was to generate data relating to the research question 'what is the extent of intra-operative pressure damage to the skin within a UK hospital setting? '. However, also pertinent was literature relating to the use of risk assessment tools - their predictive validity and value as descriptors of research patient populations. A quantitative descriptive study design was developed to determine post-operative incidence of pressure sore development and the reliability and predictive validity of the Braden Scale. Patients were recruited to the study according to age (=>55 years), surgery type (elective major general and vascular) and intra-operative position (supine and lithotomy). Descriptive data relating to risk, skin and peri-operative time intervals were recorded. Skin assessments amongst a sample of 26 patients identified a pre-operative prevalence of 36% - an unexpected finding, a post-operative incidence of 12.5% consistent with results from North American research and a period prevalence of 56%. The Braden Scale demonstrated good reliability and the most sensitive and specific Braden Score was determined as 19 not at risk/<19 at risk. A discussion of results identified limitations relating to the methodology adopted and issues, such as, inclusion and exclusion criteria of blanching and non blanching reactive hyperaemia and the application of the definition of incidence which lacked clarity within the literature.
γ–Secretase controls the specification of astrocytes from oligodendrocyte precursor cells via Stat3

Oligodendrocytes (OLs) and astrocytes play critical roles in a variety of brain functions. OL precursor cells (OPCs) are known to give rise to OLs as well as astrocytes. However, little is known about the mechanism by which OPCs determine their specification choice for OLs versus astrocytes in the central nervous system (CNS). Here we show that genetic inhibition of γ-secretase in OPCs reduces OL differentiation but enhances astrocyte specification. Mechanistic analysis reveals that inhibition of γ-secretase results in decreased levels of Hes1, and that Hes1 down-regulates the expression of signal transducer and activator of transcription3 (Stat3) via binding to specific regions of its promoter. We demonstrate that conditional inactivation of Stat3 in OL lineages restores the number of astrocytes in γ-secretase mutant mice. In summary, this study identifies a key mechanism which controls OPC’s specification choice for OL versus astrocyte during postnatal development. This γ-secretase-dependent machinery may be essential for the CNS to maintain the population balance between OLs and astrocytes.
Liquid biopsies using pleural effusion-derived exosomal DNA in advanced lung adenocarcinoma.

Background Recently, plasma-derived exosomal DNA (exoDNA) has been successfully used in clinical genetic testing. However, the clinical utility of pleural effusion-derived exoDNA (PE-exoDNA) was still unknown. This study aimed to assess the feasibility of using PE-exoDNA for genetic testing in patients with advanced lung adenocarcinoma. Methods Twenty PE-exoDNA samples and 18 pleural effusion-derived cell-free DNA (PE-cfDNA) samples were obtained from 20 stage IV lung adenocarcinoma patients. Using targeted next-generation sequencing (NGS) of 416 cancer-relevant genes, the genomic alterations between PE-exoDNA and PE-cfDNA were identified and compared. Results NGS results showed highly similar mutation profiles between exoDNA and cfDNA, with TP53, EGFR, PKD1, and ALK as the top 4 mutated genes in both samples. A total of 304 genetic mutations were identified in 18 cfDNA samples and 276 genetic mutations were identified in 20 exoDNA samples. Forty-seven mutations from 8 genes (EGFR, ALK, KARS, BRAF, MET, PTEN, TP53, and RB1) were identified in 18 patients who had both exoDNA and cfDNA samples. Of the 47 mutations, 43 were shared between the two types of samples, yielding a concordance rate of 89.6%. Collectively, 78% of the mutations were shared between exoDNA and cfDNA samples, and this frequency increased to 94.2% when copy number variations (CNVs) were excluded from the analysis. Conclusions In patients with advanced lung adenocarcinoma, the genetic profile of PE-exoDNA and PE-cfDNA were comparable, except for CNVs that had lower similarities between these two samples. Our findings support the clinical utility of exoDNA and could motivate further exploration of using exoDNA as an alternative source for genetic testing.
Achilles Tendon Repair by Decellularized and Engineered Xenografts in a Rabbit Model

Tendon tissue ruptures often require the replacement of damaged tissues. The use of auto- or allografts is notoriously limited due to the scarce supply and the high risks of immune adverse reactions. To overcome these limitations, tissue engineering (TE) has been considered a promising approach. Among several biomaterials, decellularized xenografts are available in large quantity and could represent a possible solution for tendon reconstruction. The present study is aimed at evaluating TE xenografts in Achilles tendon defects. Specifically, the ability to enhance the biomechanical functionality, while improving the graft interaction with the host, was tested. The combination of decellularized equine-derived tendon xenografts with or without the matrix repopulation with autologous bone marrow mesenchymal stem cells (BMSCs) under stretch-perfusion dynamic conditions might improve the side-to-side tendon reconstruction. Thirty-six New Zealand rabbits were used to create 2 cm long segmental defects of the Achilles tendon. Then, animals were implanted with autograft (AG) as the gold standard control, decellularized graft (DG), or in vitro tissue-engineered graft (TEG) and evaluated postoperatively at 12 weeks. After sacrifice, histological, immunohistochemical, biochemical, and biomechanical analyses were performed along with the matrix metalloproteinases. The results demonstrated the beneficial role of undifferentiated BMSCs loaded within decellularized xenografts undergoing a stretch-perfusion culture as an immunomodulatory weapon reducing the inflammatory process. Interestingly, AG and TEG groups exhibited similar results, behaved similarly, and showed a significant superior tissue healing compared to DG in terms of newly formed collagen fibres and biomechanical parameters. Whereas, DG demonstrated a massive inflammatory and giant cell response associated with graft destruction and necrosis, absence of type I and III collagen, and a higher amount of proteoglycans and MMP-2, thus unfavourably affecting the biomechanical response. In conclusion, this in vivo study suggests a potential use of the proposed tissue-engineered constructs for tendon reconstruction.
Sinonasal Anatomical Variations and Primary Acquired Nasolacrimal Duct Obstruction: A Single Centre, Case-Control Investigation.

Objective Primary acquired nasolacrimal duct obstruction (PANDO) is an idiopathic narrowing of the nasolacrimal duct caused by chronic inflammation and consecutive stenosis of the nasal tissue. In the current investigation, we aimed to study the etiopathogenic role of sinonasal anatomical abnormalities and paranasal inflammatory pathologies in PANDO. Materials and Methods Computed tomography (CT) findings of 459 patients who were diagnosed with unilateral PANDO between April 2009 and March 2017 were compared with that of a control group, which comprised 200 subjects without nasolacrimal duct obstruction who had been referred to the ear nose throat (ENT) clinic with the complaint of vertigo and headache. A radiologist (R. S.) masked to the clinical situation of participants retrospectively examined their CT findings. Results The prevalence of deviated nasal septum was found to be strongly associated with PANDO incidence (55.3% on PANDO side of patients vs. 28.3% among controls; p<0.001). Significant increases, albeit of smaller magnitude, were also observed in the relative frequency of Agger nasi cells and maxillary sinusitis on the PANDO side of the subjects (14.6% and 27.0%, respectively) compared to controls (9.5% and 20.6%, respectively) (p=0.023 and p=0.038, respectively). Unilateral PANDO was also found to be robustly associated with an ipsilateral deviated nasal septum (p<0.001). The odds of septal deviation occurrence were 3.037 times (95% Confidence Interval (CI): 2.303-3.990; p<0.001) more on the PANDO than the non-PANDO side of the studied cases. Conclusion Ipsilaterally deviated nasal septum appears to have a role in the development of unilateral primary acquired obstructive disease of the lacrimal drainage system. The incidence of PANDO might also be affected by Agger nasi cells and maxillary sinusitis. Multicenter studies are essential to further elucidate the interaction between type, severity, extent, and dimensions of different pathologies with nasolacrimal duct obstruction.
CmVPS41 Is a General Gatekeeper for Resistance to Cucumber Mosaic Virus Phloem Entry in Melon

Melon production is often compromised by viral diseases, which cannot be treated with chemicals. Therefore, the use of genetic resistances is the main strategy for generating crops resistant to viruses. Resistance to Cucumber mosaic virus (CMV) in melon is scarcely described in few accessions. Until recently, the only known resistant accessions were Freeman’s Cucumber and PI 161375, cultivar Songwhan Charmi (SC). Resistance to CMV in melon is recessive and generally oligogenic and quantitative. However, in SC, the resistance to CMV strains of subgroup II is monogenic, depending only on one gene, cmv1, which is able to stop CMV movement by restricting the virus to the bundle sheath cells and preventing a systemic infection. This restriction depends on the viral movement protein (MP). Chimeric viruses carrying the MP of subgroup II strains, like the strain LS (CMV-LS), are restricted in the bundle sheath cells, whereas those carrying MP from subgroup I, like the strain FNY (CMV-FNY), are able to overcome this restriction. cmv1 encodes a vacuolar protein sorting 41 (CmVPS41), a protein involved in the transport of cargo proteins from the Golgi to the vacuole through late endosomes. We have analyzed the variability of the gene CmVPS41 in a set of 52 melon accessions belonging to 15 melon groups, both from the spp melo and the spp agrestis. We have identified 16 different haplotypes, encoding 12 different CmVPS41 protein variants. Challenging members of all haplotypes with CMV-LS, we have identified nine new resistant accessions. The resistance correlates with the presence of two mutations, either L348R, previously found in the accession SC and present in other three melon genotypes, or G85E, present in Freeman’s Cucumber and found also in four additional melon genotypes. Moreover, the new resistant accessions belong to three different melon horticultural groups, Conomon, Makuwa, and Dudaim. In the new resistant accessions, the virus was able to replicate and move cell to cell, but was not able to reach the phloem. Therefore, resistance to phloem entry seems to be a general strategy in melon controlled by CmVPS41. Finally, the newly reported resistant accessions broaden the possibilities for the use of genetic resistances in new melon breeding strategies.