Miracle-dz/UniFAR-FTUs huggingface dataset:
Frecuencia del gen qacEΔ1 y resistencia a biocidas en aislamientos clínicos de enterobacterias productoras de β-lactamasas de espectro extendido

Objetivo: Determinar la frecuencia del gen qacE? 1 y caracterizar la resistencia a biocidas en aislamientos clinicos de enterobacterias productores de s-lactamasas de espectro extendido (EP-BLEE) causantes de infecciones nosocomiales. Material y metodos: Se incluyo un total de 59 EP-BLEE correspondiendo a Klebsiella pneumoniae (35) y Enterobacter cloacae (24). Se determino la concentracion minima inhibitoria (CMI) para clorhexidina (CHX) y cloruro de benzalconio (CLBZ). Se detectaron los genes tipo-SHV, TLA-1 y qacE? 1 por PCR y secuenciacion nucleotidica, se identifico el patron plasmidico y se realizo la conjugacion bacteriana. Resultados: Todos los aislamientos de EP-BLEE fueron resistentes a CHX y 80% para CLBZ. El 68% de los aislamientos resistentes a biocidas presentaron el gen qacE? 1, los cuales se sometieron a conjugacion. De las transconjugantes resultantes 66% fueron resistentes a CHX y se detecto en ellas el gen qacE? 1 en 55%. Conclusiones: El gen qacE? 1 de resistencia a antisepticos esta ampliamente diseminado en las EP-BLEE y puede ser transferido de manera horizontal. Por esa razon es ampliamente recomendable utilizar combinaciones de antisepticos, como se describe en la literatura, que permita en cierta medida contrarrestar la seleccion de bacterias multirresistentes en los hospitales y al mismo tiempo disminuir los indices de infecciones nosocomiales.
Using Neem to Control Charcoal Rot of Chickpea

i Acknowledgements . iv Chapter 1: General Introduction . 1 Nutrition Value of Chickpea . 1 Charcoal Root Rot (Macrophomina phaseolina) . 2 Using neem extract to control soil borne fungi . 3 The aims of this study . 4 Thesis Outline . 5 Chapter 2: Literature review. 6 Chickpea (Cicer arietinum L.) . 6 The chickpea crop . 6 Mutualistic symbionts of chickpea . 7 Rhizobia . 7 Mycorrhizas . 8 Arbuscular mycorrhiza fungi (AMF) of chickpea . 9 Root exudates of chickpea . 9 Root exudates and rhizosphere . 10 Impacts of root exudates on soil microbial communities . 10 Chickpea diseases . 11 Ascochyta blight . 12
Measuring chromosome conformation by fluorescence microscopy

Measurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by ‘connecting the dots’. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.
Improved outcome following reduced intensity allogeneic transplantation in Hodgkin's lymphoma relapsing post-autologous transplantation

Hodgkin’s Lymphoma is curable with primary therapy in the majority of patients. For those with relapsed or refractory disease, salvage with high dose chemotherapy plus autologous stem cell rescue is effective for a significant proportion. Patients relapsing following autologous stem cell transplantation, however, have an extremely poor prognosis. Allogeneic transplantation with conventional conditioning has proved excessively toxic in this setting, and reduced intensity conditioning has therefore been introduced, with encouraging preliminary results. This is a study of 72 patients relapsing following autologous transplantation, analysed in 2 groups. One group (A: n=38) then underwent allogeneic transplantation with reduced intensity conditioning at 6 UK centres (1998–2004), with alemtuzumab 100mg, fludarabine 150mg/m2 and melphalan 140mg/m2. Donors were HLA-matched related in 63% of cases, and unrelated in the remaining 37%. The second group (B: n=34) is a control cohort, who relapsed before the advent of reduced intensity conditioning, and were treated with chemotherapy +/− radiotherapy alone. The groups were equivalent in age (median- A 31yrs [20–51]; B 29yrs [13–47]), disease subtype (>85% nodular sclerosing both groups), time from diagnosis to autograft (median-A 18mo [7–139]; B 20mo [4–185]), and lines of prior therapy pre-autograft (median 3 both groups). Median time from autograft to relapse for group A was 13mo (2–56) and for group B 10mo (3–40), and patients were only selected for inclusion in group B if they responded to further salvage therapy, attained at least a stable response to treatment, and lived for >12 months following relapse (median time from relapse to allogeneic transplant for group A is <12 months). In this way, it was intended to include only those patients who would have been eligible for reduced intensity allogeneic transplantation had this been available at the time. Indeed, the entry criteria for group A were arguably less stringent, as patients with chemorefractory disease were included (n=14, 37%). Overall survival from diagnosis was significantly better in group A, with actuarial survival at 10yrs of 48% compared to 15% in group B (p=0.0014), and overall survival from autograft was 65% at 5 yrs in group A and 15% in group B (p=<0.0001). Of group B patients treated with chemotherapy/RT alone, only 2/34 patients remain alive at a median follow-up of 22 months from relapse, one of whom has progressive disease. For group A receiving reduced intensity transplantation, actuarial survival from the time of allograft was 50% at 5 yrs. In the chemoresponsive patients, OS at 5yrs was 57% at 5 yrs with current progression-free survival of 39% at 5 yrs. This demonstration of the potential efficacy of reduced intensity transplantation in a group of heavily pre-treated patients who have failed autograft and whose outlook is otherwise extremely poor, strongly suggests further studies of reduced intensity allogeneic transplantation in Hodgkin’s Lymphoma are warranted.
Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides

Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418 treatment globally alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1).
Fish fauna from the Paranapanema River basin, Brazil

The Paranapanema River is an important, extensively explored tributary of the Upper Paraná River basin. The fish fauna of the Paranapanema River has been investigated since the 1990s; however, no study has characterized the richness of fish species throughout the basin, including the main channel of the river, marginal lagoons, its tributaries, and sub-tributaries. Thus, we performed a review with 90 independent studies conducted at the upper, middle, and lower sections of the basin. We recorded 225 species, of which 165 were native, and 60 were non-native. We found that 77% of the species within the basin are composed by Siluriformes and Characiformes. Cichliformes had a significant number of non-native species established in impoundment sections of the basin. Incidence-Based Estimators (Bootstrap and Chao 2) demonstrated that the richness of native species is still underestimated. Some native (e.g., Hypostomus ancistroides) and non-native species (e.g., Plagioscion squamosissimus) are widely distributed in the basin, while others had a more restricted distribution. Among the registered species, the family Bryconidae had the highest number of representatives with threatened conservation status. In addition, we observed that the Capivara Reservoir and its tributaries were the most sampled regions, with the majority of studies performed in the Lower Paranapanema basin. The species richness recorded in large tributaries, such as Tibagi, Cinzas, Congonhas, and Pirapó rivers is critical for maintaining the fish fauna in the Paranapanema River. Our contribution may be used to support management actions and conservation strategies, as well as to indicate regions in the basin that need to be better inventoried.
Glycemic Index of Five Ghanaian Corn and Cassava Staples

Glycemic index (GI) quantifies and measures the blood glucose raising effect of a food containing a specific amount of carbohydrate. Due to this concerns have been raised on the quality of carbohydrate and the indices that influence its metabolism. The objective of study was to investigate the effect of processing on the glycemic index of five Ghanaian corn and cassava staples. The research design was a cross over trial. Ten healthy subjects consisting of five males and five females were included in the study. Study subjects were served 50g of pure glucose containing 50g of available carbohydrate and 200ml of pure water. Glucose which served as the reference food was given to subjects on two different occasions. The subjects were also served specific 50g of abolo, akple, kafa, local kokonte and processed kokonte on specific days. The glycemic index figures were assessed by using official methods and reported as mean for the ten study subjects. Locally made kokonte had the least GI of 7 followed by processed kokonte which had a GI of 18 whiles kafa had a low GI of 29. Abolo had a medium GI value of 58 and akple also had a medium glycemic index value of 69. There was no significant difference between the GI of locally made kokonte and processed kokonte (p > 0.05) indicating processing had no significant effect on the GI of kokonte.
Current scenario of viral diseases in Turkish poultry industry

The Turkish poultry industry has rapidly developed in the last decade. Viral pathogens continue to threaten the industry, causing economic losses worldwide, including Turkey. At present, infectious bronchitis and infectious laryngotracheitis are major challenges, as are, to a lesser extent, avian metapneumovirus, infectious bursal disease, Marek's disease and chicken infectious anaemia. The prevalence and severity of these diseases in Turkish chickens varies depending on environmental and management factors, vaccination strategies and biosecurity measures. In Turkey, infectious bronchitis virus, including vaccine and field strains, were detected in 83.6% (41/49) and 64.2% (9/14) vaccinated broiler and layer flocks, respectively. Virulent and vaccine strains of infectious bursal disease virus were found in 83.5% (1548/1855) of excised bursa Fabricius from vaccinated broilers. Virulent Marek's disease virus was found in 19.93% (120/620) of spleens from vaccinated chickens. Infectious laryngotracheitis virus in commercial poultry and Newcastle disease in backyard chickens have been detected. To date, Newcastle disease and avian influenza virus have not been reported in commercial poultry. Avian metapneumovirus was found in 7.2% (8/110) of the broiler samples. Antibodies to gyrovirus and avian leukosis virus have been detected. Commercial vaccines, such as attenuated, inactivated and vectored vaccines, are being used for prevention and control of viral poultry diseases in Turkey. This review summarises the available information on viral poultry diseases in Turkey. It highlights the need to strengthen surveillance and reporting for diseases and addresses the vaccination practices used in Turkish poultry industry. The future prospects of vaccination and need to empower diagnostic capacity in controlling viral poultry diseases are discussed. The information presented here is aimed at improving research, prevention, and control of poultry diseases for researchers, veterinarians, policy makers and other professions related to poultry industry.
Pitch of Harmonic Complex Tones: Rate-Place Coding of Resolved Components in Harmonic and Inharmonic Complex Tones in Auditory Midbrain

Harmonic complex tones (HCT) commonly occurring in speech and music evoke a strong pitch at their fundamental frequency (F0), especially when they contain harmonics individually resolved by the cochlea. When all frequency components of an HCT are shifted by the same amount, the pitch of the resulting inharmonic tone (IHCT) also shifts although the envelope repetition rate is unchanged. A rate-place code whereby resolved harmonics are represented by local maxima in firing rates along the tonotopic axis has been characterized in the auditory nerve and primary auditory cortex, but little is known about intermediate processing stages. We recorded single neuron responses to HCT and IHCT with varying F0 and sound level in the inferior colliculus (IC) of unanesthetized rabbits. Many neurons showed peaks in firing rates when a low-numbered harmonic aligned with the neuron’s characteristic frequency, demonstrating “rate-place” coding. The IC rate-place code was most prevalent for F0>800 Hz, was only moderately dependent on sound level over a 40 dB range, and was not sensitive to stimulus harmonicity. A spectral receptive-field model incorporating broadband inhibition better predicted the neural responses than a purely excitatory model, suggesting an enhancement of the rate-place representation by inhibition. Some IC neurons showed facilitation in response to HCT, similar to cortical “harmonic template neurons” (Feng and Wang 2017), but to a lesser degree. Our findings shed light on the transformation of rate-place coding of resolved harmonics along the auditory pathway, and suggest a gradual emergence of harmonic templates from low to high processing centers. Significance statement Harmonic complex tones are ubiquitous in speech and music and produce strong pitch percepts in human listeners when they contain frequency components that are individually resolved by the cochlea. Here, we characterize a “rate-place” code for resolved harmonics in the auditory midbrain that is more robust across sound levels than the peripheral rate-place code and insensitive to the harmonic relationships among frequency components. We use a computational model to show that inhibition may play an important role in shaping the rate-place code. We also show that midbrain auditory neurons can demonstrate similar properties as cortical harmonic template neurons. Our study fills a gap in understanding the transformation in neural representations of resolved harmonics along the auditory pathway.
Role of spiritual Beliefs and prayer in health promotion of chronic patients: A qualitative study

Aims: Chronic diseases are the major cause of mortality all over the world. Long-term nature of chronic diseases causes the goal of treatment in these diseases to be shifted from the elimination and eradication of the disease to the maintenance of the function. Maintenance of the function requires the medical care close communication, social support services, educational services and health promotion. The purpose of this study was qualitative investigation of the role of spiritual beliefs in the promotion of the health of the patients. Methods: Using the qualitative study approach of content analysis type, 35 patients with cardiovascular diseases and diabetes, referred to the education-treatment centers of Tehran University of Medical Sciences, who had been chosen based on the purposive method, were interviewed. Line by line analysis of the information obtained was done using the constant comparison and information recall-writing methods. Results: The 5 main categories of "spiritual beliefs and lifestyle", "spiritual beliefs and self-efficacy", "spiritual beliefs as an adaptation mechanism", "religious practices positive effects on mental health of patients" and "spiritual beliefs challenge" were extracted from the analysis of the data. In some patients, with increasing the duration of illness, spiritual beliefs decreased. Conclusion: The spiritual beliefs, in addition to facilitate the exposure of patients with negative psychological effects of chronic disease, reduce the patients' depression and increase their satisfaction with life. Spiritual beliefs not only affect the coping with the disease, but also these beliefs play an important role in the lifestyle of patients and by creating the feeling that affairs have a definite goal, increase the patients' linkage to the treatment regimen. Religious practices are also used t by patients as a consolatory agent to reduce anxiety, pain and depression.
The Early Experience with a Totally Laparoscopic Distal Gastrectomy

Purpose: In Korea, the number of laparoscopy-assisted distal gastrectomies for early gastric cancer patients has been increasing lately. Although minimally invasive surgery is more beneficial, no reported case of a totally laparoscopic distal gastrectomy has been reported because of difficulty with intracorporeal anastomosis. This study attempts, through our experiences, to determine the feasibility of a totally laparoscopic distal gastrectomy using an intracorporeal gastroduodenostomy in treating early gastric carcinoma. Materials and Methods: We investigated surgical results and clinicopatholgic characteristics of eight(8) patients with an early gastric carcinoma who underwent a totally laparoscopic distal gastrectomy at the Department of Surgery, Our Lady of Mercy Hospital, The Catholic University of Korea, between June 2004 and September 2004. The intracorporeal gastroduodenostomy was performed with a delta-shaped ananstomosis by using only laparoscopic linear staplers (Endocutter 45mm; Ethicon Endosurgery, OH, USA). Results: The operative time was minutes (range minutes), and the anastomotic time was minutes (range minutes). The anastomotic time was shortened as surgical experience was gained. The number of laparoscopic linear staplers for an operation was . The number of lymph nodes harvested was . There was 1 case of transfusion and no case of conversion to an open procedure. The time to the first flatus was 2.80. 5 days, and the time to the first food intake was days. There were no early postoperative complications, and the postoperative hospital stay was days. Conclusion: A totally laparoscopic distal gastrectomy using an intracorporeal gastroduodenostomy with a delta-shaped anastomosis is technically feasible and can maximize the benefit of laparoscopic surgery for early gastric cancer.
Regulation of FXR1 by alternative splicing is required for muscle development and controls liquid-like condensates in muscle cells

Fragile-X mental retardation autosomal homolog-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and mis-splicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine and arginine-rich intrinsically-disordered domain; these domains are known to promote biomolecular condensation. Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNA-dependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease. HIGHLIGHTS The muscle-specific exon 15 impacts FXR1 functions Alternative splicing of FXR1 is tissue- and developmental stage specific FXR1 forms RNA-dependent condensates Splicing regulation changes FXR1 condensate properties
Surfactant proteins and cytokines in inflammation-induced preterm birth : experimental mouse model and study of human tissues

Prematurity is the main cause of morbidity and mortality in infants. In 25–40% of the cases preterm birth is associated with intrauterine inflammation. Surfactant proteins (SPs) A, C, and D have roles in innate immunity. In the female reproductive tract and in amniotic fluid (AF), these proteins may modulate the inflammatory responses leading to preterm birth. The aim of the present study was to establish a mouse model of lipopolysaccharide (LPS)induced preterm birth of live-born pups and to study the activation of the innate immune system. By using mice overexpressing either rat SP-A (rSP-A) or rSP-D the roles of SP-A and SP-D in inflammatory responses were investigated. In addition, the expression of SP-C in gestational tissues was analyzed. The association of SP-C single nucleotide polymorphism (Thr138Asn) with spontaneous preterm birth and preterm premature rupture of membranes (PPROM) was investigated in a homogenous northern Finnish population of mothers and infants. Wild-type (WT) mice were injected with a single dose of intraperitoneal LPS at 16 or 17 days of gestation (term 19–20 days) leading to preterm delivery of live-born fetuses. After LPS, cytokine levels increased rapidly in maternal serum and in the uterus. This maternal inflammatory response was followed by the modest inflammatory activation in fetal and feto-maternal compartments. In fetal lung the expression of SP-A and SP-D was downregulated. The overexpression of SP-A or SP-D was evident in gestational tissues of rSP-A or rSP-D mice, respectively. In addition, excess of these proteins was detected in AF. Overexpression of either rSP-A or rSP-D modulated the LPS-induced inflammatory response related to preterm birth. Most notably, the expression of IL-4 and IL-10 in uteri and IL-10 in fetal membranes was lower in overexpressing animals. SP-C was detected in mouse and human placentas, fetal membranes, and in uteri of pregnant mice. The fetal SP-C polymorphism strongly associated with the duration of PPROM. The present study provides new information about the molecular events in inflammation induced preterm birth, particularly about the roles of cytokines and SPs in this process. Understanding of the mechanisms involved in preterm parturition may provide means for prevention and management of preterm births in the future.
Complete mitochondrial genome and the phylogenetic position of the stellate puffer (Arothron stellatus)

Abstract The complete mitochondrial genome of the stellate puffer (Arothron stellatus) was first determined in this study. It was a 16,475 bp circular molecule and consisted of 37 genes with typical gene order in vertebrate mitogenome. Its nucleotide content was 29.0% A, 32.0% C, 15.9% G and 23.1% T. This mitogenome had 30 bp short intergenic spaces located in 12 gene junctions and 28 bp overlaps located in 7 gene junctions. In the protein-coding genes, two start codons (GTG and ATG) and two stop codons (TAG and TAA/TA/T) were found. The 22 tRNA genes ranged from 64 bp (tRNA-Cys) to 74 bp (tRNA-Leu1 and tRNA-Lys). The phylogenetic result showed that Takifugu xanthopterus was most closely related to the reef-related A. stellatus among all Tetraodontiformes species.