Miracle-dz/UniFAR-FTUs huggingface dataset:
Feasibility of molecular testing in a multicenter study with geographical variation in India: Epidermal growth factor receptor mutation as a model molecular test

Abstract Context: Trends in epidermal growth factor receptor (EGFR) mutation based on ethnicity assist the initial selection of targeted therapy regimen. Reported incidence of EGFR mutation in Indian NSCLC patients is variable, ranging from 22% to 51.8%. Aim and Settings and Design: This multicenter, noninterventional study evaluated the prevalence of EGFR mutation in Indian NSCLC patients, its association with patients’ demographics, and for the first time used a central laboratory for molecular testing. Subjects and Methods: Tissue samples from 252 NSCLC patients were tested at a Central Laboratory at Tata Memorial Hospital. Statistical Analysis Used: Patient demographics, baseline characteristics including smoking status from routine examination were recorded in a single visit. Chi-square or Fisher's exact test was used for association of EGFR mutation status with gender, age, smoking status, and histological subtypes. Results: The prevalence of EGFR mutation in Indian NSCLC patients was 23.4%. Among these, 55.9% patients had mutations in exon 19, 39% in exon 21, and 1.7% in exon 18. The incidence of EGFR mutation was higher in females than males (32.5% vs. 18.9%, respectively), and in 30.6% patients that had never smoked, 26.3% smokers, and 5.8% former smokers. The mean duration of transportation of tissue samples to the central laboratory was 48 h with an average turnaround time of 5 days for molecular testing. Conclusions: Molecular testing at a central laboratory is a feasible option in India. Prevalence of EGFR mutation in Indian NSCLC patients was similar across western and southern centers in India. A statistically significant association between EGFR mutation and gender as well as the smoking status of the patients was observed. Majority of the patients had in-frame deletions in exon 19.
Unravelling direct and indirect effects of hierarchical factors driving microbial stream communities

The diversity and distributions of organisms are jointly influenced by local environment and large‐scale variables, such as land cover patterns, dispersal processes and climate. However, the drivers of microbial diversity are complex and the pathways of these drivers’ effects are to date largely unresolved, especially in freshwaters. We disentangled the causal direct and indirect effects of climate, land cover and water chemistry on stream diatom communities using hierarchical settings.
Characterization of mRNA export and nuclear quality control under heat stress in the yeast Saccharomyces cerevisiae

Elevated temperatures and other changes of the environment a cell lives in, can have tremendous impact on cellular processes and integrity. To counteract these threats, cells have established various mechanisms to avoid severe damage and ensure survival. One of them is the highly-conserved heat shock response that results in expression of a special set of proteins among them chaperones, which aid denatured proteins in refolding and protect them from further destruction. This response to heat stress is accompanied by the disruption of normal cellular processes like general mRNA transcription, splicing and export in the nucleus and translation of housekeeping transcripts in the cytoplasm. This study analyzed by what mechanisms the cell can distinguish between normal mRNAs that need to be blocked in the nucleus and stress responsive transcripts, which are required to be exported and translated. Several experiments show that while the normal mRNA export relies on the support of the shuttling adaptor proteins Npl3, Gbp2, Hrb1 and Nab2, a general dissociation of these proteins together with the export receptor Mex67 from mRNAs can be observed under stress, which explains the mRNA export block. Heat stress (HS) mRNAs in turn are exported by direct binding of Mex67 without the need of any known adaptor. This preferential binding of Mex67 to mRNAs expressed under heat stress is most likely facilitated through its early recruitment by the heat shock transcription factor Hsf1. Further experiments revealed that replacing the promoter of a normal mRNA with a stress responsive promoter and even artificially inserting an Hsf1 binding site can turn a housekeeping mRNA in a heat stress responsive transcript. All these mRNAs, strongly expressed under heat stress, strikingly bypass nuclear quality control and are quickly exported. Under normal conditions faulty mRNAs are labeled by the Mtr4-containing TRAMP complex and degraded by the nuclear Rrp6-containing exosome. Detection of errors in normal mRNAs is most likely coupled to the adaptor proteins, which might control correctness of every maturation step. As mRNA adaptor proteins are dispensable during HS mRNA transcription and export, this appears to be the mode of how heat stress transcripts evade to be quality controlled. These mechanisms probably result in two different mRNA export ways: under normal conditions adaptor proteins facilitate a close quality control of an mRNA before Mex67 can associate and perform export, while upon heat stress direct binding by Mex67 results in a fast export of HS mRNAs that are not controlled for their quality. Thus, even though more faulty HS mRNA reach the cytoplasm, the fast response to stress appears to be more beneficial for survival.
Isolation and Characterization of Escherichia coli from Animals, Humans, and Environment

Working on a diverse species of bacteria that have hundreds of pathotypes representing hundreds of strains and many closely related family members is a challenge. Appropriate research design is required not only to achieve valid desired outcome but also to minimize the use of resources, including time to outcome and intervention. This chapter outlines basics of Escherichia coli isolation and characterization strategies that can assist in research designing that matches the set objectives. Types of samples to be collected, collection and storage strategies, and processing of samples are described. Different approaches to isolation, confirmation and concentration of various E . coli strains are summarized in this chapter. Characterization and typing of E . coli isolates by biochemical, serological, and molecular methods have been explained so that an appropriate choice is made to suite a specific E . coli strain/pathotype. Some clues on sample and isolate preservation for future use are outlined, and general precautions regarding E . coli handling are also presented to the researcher to avoid improper planning and execution of E . coli -related research. Given different options, the best E . coli research design, however, should try as much as possible to shorten the length of time to outcomes. of is into glucose phosphate a
Social aggregation of the marine isopod Cirolana harfordi does not rely on the availability of light‐reducing shelters

Social aggregation under shelters can afford benefits to animals such as protection from predators. Many isopods and insects are negatively phototactic and this may help them gravitate towards shelter. Previous studies show that, when placed in an arena with two red shelters, specimens of the marine isopod Cirolana harfordi and the terrestrial isopod Porcelio scaber pick one of the two shelters at random and aggregate under it, demonstrating social aggregation under light‐reducing shelters. In the present study, an arena with two clear shelters was used to determine whether group sizes of 4, 8, 12 and 16 C. harfordi specimens display social aggregation when the shelters do not accommodate negative phototaxis. In all group sizes, C. harfordi specimens picked one of the shelters at random and significantly more animals aggregated under this shelter compared with the other. Cirolana harfordi also displayed aggregation in an arena with no shelters. Accordingly, C. harfordi specimens do not require shelters that reduce light to display social aggregation. The ability to locate suitable shelter under which there is no substantial reduction in light could benefit the animal in a natural environment comprising heavily shaded areas, as well as at night.
Bean Leaf Beetle: Impact of Leaf Feeding Injury on Snap Beans, Host Plant Choice and Role as a Vector of Bean Pod Mottle Virus in Virginia

The bean leaf beetle (BLB), Cerotoma trifurcata (Forster) (Coleoptera: Chrysomelidae), is a pest of commercially produced legumes in eastern Virginia and much of the soybean production areas of the United States. To better understand the economic injury level of this pest for snap bean production, field cage and manual-defoliation studies were conducted in Virginia. In the manual-defoliation study, snap bean plants had significant yield loss when > 25% of leaf area was removed over a two week period. In the field cage experiments, I was unable to establish beetle densities per plant that were significant enough to impact yield despite releasing up to 1,000 beetles in a cage with 60 bean plants. BLB densities averaged 2.7 BLB per plant in those high density cages. To better understand host plant selection by BLB, laboratory and field choice experiments were conducted in snap bean, lima bean, and soybeans. Laboratory studies paired snap bean, lima bean and soybean leaf discs from plants of the same age. The field study paired the three legume species with different age groups as well as species for a total of 15 paired combinations. In laboratory studies, BLB preferred snap bean and lima bean over soybean. Field studies did not show a significant effect of bean species or age. Beetles preferred large mature (V4) foliage over small immature foliage (V1). Beetles also showed a preference for snap bean and lima bean plants over soybeans for both large and small plants. Bean leaf beetles impact yield of soybeans directly by feeding on leaves, stems and pods, and indirectly by transmitting Bean pod mottle virus (Secoviridae: Comovirus) (BPMV). A survey was conducted on the Eastern Shore of Virginia to see if the epicenter of the virus was the Eastern Shore Agricultural Research and Extension Center (ESAREC). Fields were selected based on distances from the ESAREC and soybean leaves and bean leaf beetles were collected and assessed for BPMV by immunoassay using enzyme-linked immunosorbant assay (ELISA) or tissue blot immunosorbant assay (TBIA). BPMV-positive beetle ELISA extracts were mechanically inoculated to soybeans and was able to infect BPMV to soybeans. These
A receptor-like protein acts as a specificity switch for the regulation of stomatal development

In Arabidopsis, stomatal patterning is specified by the ERECTA family (ERf) receptor kinases (RKs), the receptor-like protein (RLP) TOO MANY MOUTHS (TMM), and EPIDERMAL PATTERNING FACTOR (EPF) peptides. Here, Lin et al. show that TMM dictates the specificity of ERfs for perception of different EPFs, thus functioning as a specificity switch for the regulation of the activities of ERfs.
A simple method for measuring fungal metabolic quotient and comparing carbon use efficiency of different isolates: Application to Mediterranean leaf litter fungi

Abstract The metabolic efficiency of different microbial groups in carbon source uses and single species storage efficiency is poorly characterised and not adequately represented in most biogeochemical models. It is proposed here a simple approach for an estimation of the metabolic quotient of fungal isolates. The method is based on the values of substrate use (respiration) and growth (biomass production) obtainable for single fungal isolates in vitro using the Phenotype MicroArray™ system to test the metabolic performance of fungi on different substrates. As a case study, this carbon-use efficiency method was used to compare a group of leaf litter fungi. The metabolic efforts of single fungal species were measured on 95 different substrates of different complexity. The respiration to biomass ratio showed a high reliability and the possibility of being used as a measurable property of the micro-organisms and an indicator of organism’s performance or fitness.
Influence of pineapple, apple and melon by‐products on cookies: physicochemical and sensory aspects

Summary Physicochemical and sensory effects were investigated regarding the partial substitution of wheat flour in cookies with flours made of pineapple, apple and melon by-products, in the concentrations 5%, 10% and 15%. Cookies with 15% of melon flour were prominent in relation to the nutritional aspects, especially about the contents of fibres (4.67–6.46%) and ash (1.74–2.25%). The use of these by-products resulted in slightly darker cookies, with variations in diameter and in the expansion factor. There was a positive influence of the use of the pineapple by-product concerning consumers' preference. Additionally, the cookies with 15% of pineapple by-product presented the highest acceptance rate (97%) and buying intention (53%). Therefore, the use of fruit by-products in the development of cookies is a viable alternative which can be explored for nutritional, technological and sensory purposes by the food industry.
A modification of the arcsine–log calibration curve for analysing soil test value–relative yield relationships

Abstract. This article aims to discuss the arcsine–log calibration curve (ALCC) method designed for the Better Fertiliser Decisions for Cropping Systems (BFDC) to calibrate relationships between relative yield (RY) and soil test value (STV). Its main advantage lies in estimating confidence limits of the critical value (CSTV). Nevertheless, intervals for 95% confidence level are often too wide, and authors suggest a reduction in the confidence level to 70% in order to achieve narrower estimates. Still, this method can be further improved by modifying specific procedures. For this purpose, several datasets belonging to the BFDC were used. For any confidence level, estimates with the modified ALCC procedures were always more accurate than the original ALCC. The overestimation of confidence limits with the original ALCC was inversely related to the correlation coefficient of the dataset, which might allow a relatively simple and reliable correction of previous estimates. In addition, because the method is based on the correlation between STV and RY, the importance to test it for significance is emphasised in order to support the hypothesis of a relationship. Then, the modified ALCC approach could also allow a more reliable comparison of datasets by slopes of the bivariate linear relationship between transformed variables.
Neuroanatomical Mapping of s100 Immunoreactivity Reviewed

S100B is a small calcium-binding protein expressed primarily by astrocytes involved in several pathologies. Several studies have shown S100B protein immunoreactivity (S100B-IR) in brain specific areas, and some of them showed the cells identity under physiological and/or pathological conditions. This review reports the S100BIR distribution in the brain specific areas of different adult mammals and complement with our results in order to provide a complete overview about the S100B-IR distribution and cell identity. This review highlights a heterogeneous distribution of S100B-IR in prosencephalic, diencephalic, brainstem and cerebellum areas. Regarding cellular identity, the co-localization of S100B-IR and GFAP-IR occurred predominantly in periventricular areas, in the hippocampus and the septal area in contrast with cortical regions. In addition, cells S100B-IR but not GFAP-IR were also found in these areas. The analysis throughout the rostro-caudal axis of the brain showed that S100B-IR did not present colocalization with neurons (NeuN-IR). This complete description can be potentially used for researches that aim to consider changes in S100B expression in different pathologies.
Gene Frequencies of Haemoglobin Variants in Amorji Community of Enugu State, South East, Nigeria

Nine hundred and seventy three randomly selected volunteer residents of Amorji Nike community, in Enugu East Local Government area of Enugu State, Nigeria were screened for their haemoglobin genotypes. Six haemoglobin genotypes exist in the community. Persons homozygous for normal adult haemoglobin, HbAA were highest in haemoglobin frequency (64.3%) followed by the heterozygotes HbAs (24.8%), and HbAc (6.8%). Sicklers gave percentage frequencies of 0.7%, 1.1%, and 2.3%. For Hbcc, and Hbss respectively.
Mesenchymal Stem Cells: A Future Option for Intervening Disease Management

Regeneration, revitalizing and reversal (RRR) are the primordial functions of the stem cells in the field of regenerative medicine. Though there are several cases of successful stem cell transplantation the reversal of metabolic diseases and the acquired secondary complications like chronic renal failure, neuropathy, stroke or vascular diseases are not well studied. The transplanted cells in many cases failed to home or graft in the host with no reason to attribute for such failures. Therefore, it becomes necessary to address these secondary complications with cellular therapy. The oxidative stress of the cells and tis - sues are attributed to the hostile microenvironment, not suitable for the survival of newly recruited cells. From our few animal studies and published literatures sources elsewhere, we foresee a huge potential for using mesenchymal stem cells (MSCs) to initially com-bat the secondary cardiovascular and neuronal complications in the management of the metabolic diseases. However, not all the stem cells have been tested in these lines, and further we do not know, whether all the progenitor cells from various sources and origin will behave like MSCs, which needs to be studied extensively. regenerative medicine. Human embryonic stem (ES) cells, mesenchymal stem cells (MSCs) induced pluripotent
Preoperative oral nutritional interventions in surgery, including arginine- and glutamine-enhanced supplements

The patients’ condition prior to surgery is of major importance for clinical outcome. It is believed nowadays that artificial nutrition in the form of a preoperative drink may improve postoperative outcome. Until now, a clear overview concerning the effects of preoperative supplementation on patients’ well-being has been lacking. The aim of this review is to summarize the results of randomized clinical trials investigating the effects of different preoperative supplements such as carbohydrate (CHO)-rich beverages, oral nutritional supplements (ONSs), immunonutrition and lemonades on clinical, metabolic and immunological parameters. We reviewed the relevant articles published between 1995 and 2012. Preoperative CHO-rich drinks appear to be safe, do not affect gastric emptying time and switch the fasted state to a fed state. Moreover, a significant reduction of postoperative insulin resistance, an improved well-being of the patient and prevention of surgery-induced immunodepression was found. For ONSs, beneficial effects were found according to muscle metabolism and strength, glucose storage and cost-effectiveness. Preoperative supplementation of immunonutrition resulted in improved immune function, restricted inflammatory response after surgery, prevention of organ damage, improved nutritional status with subsequently decreased postoperative complication rates and reduced length of hospital stay. Preoperative oral supplements have beneficial effects on many aspects of patient’s well-being and recovery. Different supplements, preferably in combination with each other, can help to reduce postoperative complications after surgery and length of hospital stay. Nutritional support must not be overlooked when considering optimal surgical care.
Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine)

Abstract: Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-known Ochromonas danica were assigned to Chlorochromonas. The generic name Melkoniania gen. nov. was proposed for one distinct clade of marine flagellates. These changes addressed some of the issues associated with the polyphyletic Ochromonas sensu lato but many problems remained.
Caudicicola gracilis (Polyporales, Basidiomycota), a New Polypore Species and Genus from Finland

A new monotypic polypore genus, Caudicicola Miettinen, Kotir. & Kulju, is described for the new species C. gracilis Kotir. , Kulju & Miettinen. The species was collected in central Finland from Picea abies and Pinus sylvestris stumps, where it grew on undersides of stumps and roots. Caudicicola gracilis is characterized by very fragile basidiocarps, monomitic hyphal structure with clamps, short and wide tramal cells, smooth ellipsoid spores, basidia with long sterigmata and conidiogenous areas in the margins of the basidiocarp producing verrucose, slightly thick-walled conidia. The genus belongs to the residual polyporoid clade of the Polyporales in the vicinity of Steccherinaceae, but has no known close relatives.
Morphometric measurements and animal-performance indices in a study of racial forms of Brazilian Sport Horses undergoing training for eventing

ABSTRACT This study aimed to evaluate, in a practical manner, the use of linear and angular measurements and different animal-performance indices in a study on the breed-specific conformation of Brazilian Sport Horses training for eventing. These data can form the basis for the development of future studies based on the parameters evaluated and the calculations made. Seventeen Brazilian Sport Horses training for eventing were selected. Morphometric evaluations were made of all animals using linear and angular measurements. The linear measurements [. ]
Re-visiting Prehn's hypothesis in the human melanoma system

*Correspondence to: Giorgio Parmiani; Email: parmiani.giorgio@hsr.it Early events responsible of tumor growth in patients with a normal immune system are poorly understood. Here, we discuss, in the context of human melanoma, the Prehn hypothesis according to which a weak antitumor immune response may be required for tumor growth before weakly or nonimmunogenic tumor cell subpopulations are selected by the immune system.