Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of sequence and length polymorphism for genotyping Cryptosporidium isolates

SUMMARY Simple sequence repeat markers have played an important role in elucidating the epidemiology of human and animal cryptosporidiosis. The drawback of sequence length polymorphisms is that nucleotide substitutions remain undetected. As some laboratories have opted for using length polymorphisms, while others have relied on sequencing, there is a need to compare both methods. We used a diversified set of unique length polymorphisms and matching nucleotide sequences to assess the ability of each genotyping protocol to discern clusters of related Cryptosporidium parvum isolates. We found a weak correlation between the two distance measures for individual markers. This analysis was extended to four-locus genotypes based on sequence length data or concatenated sequences from the same loci. We interrogated these data to assess whether one would reach the same conclusions regardless of the genotyping method. Clusters of isolates generated with the concatenated sequences were not observed with amplicon length, indicating that inferences on the structure of a Cryptosporidium population depend on the genotyping method. Moreover, isolate clusters derived from concatenated sequences were dependent on the algorithm used to calculate distances. These results emphasize the need for harmonizing genotyping tools, not only by selecting informative markers, but also by standardizing the entire genotyping method.
Determination of S-phenylmercapturic acid in the urine--an improvement in the biological monitoring of benzene exposure.

In an inhalation study rats were exposed to different doses of benzene, ranging from 1 to 500 p.p.m. The urine was sampled during the inhalation period of 8 h and for 24 h after exposure. S-Phenylmercapturic acid (S-PMA) in the urine was determined by amino acid analysis. Phenol was measured by gas chromatography/mass spectrometry. In both cases the correlation between benzene uptake and the excretion of the urinary metabolites was significant at the level of P = 0.01. The same significant correlation (P = 0.01) was demonstrable after i.p. administration of benzene at doses between 0.7 and 140.0 microliters/kg body weight. In the case of two collectives of workers who were exposed to air concentrations of up to 0.15 p.p.m. for 8 h and of up to 1.13 p.p.m. for 12 h respectively, the amount of S-PMA in the first urine samples after the shift was significantly higher than in samples collected at the beginning of the shift (P = 0.01). In the first collective the mean values and the standard deviations of the S-PMA concentrations in the samples at the beginning of the shift were 12.0 +/- 16.7 compared with 48.5 +/- 64.5 micrograms/g creatinine at shift end. In the second collective they were 25.1 +/- 25.1 compared with 70.9 +/- 109.2 micrograms/g creatinine. The level of significance of the difference between the concentration values of S-PMA at the beginning and end of the shift was P = 0.01. The phenol concentration did not differ significantly. These results suggest that S-PMA can be regarded as a useful indicator for monitoring individuals and collectives exposed to benzene at levels even less than 1 p.p.m.
The effect of antidepressant treatment on chronic back pain: a meta-analysis.

BACKGROUND Back pain is one of the most common problems in primary care. Antidepressant medication is often prescribed, especially for chronic back discomfort, to alleviate pain and restore the patient's ability to conduct activities of daily living. OBJECTIVE To assess the efficacy of antidepressants in treating back pain in adults. METHODS We searched the MEDLINE (1966-2000), PsycLit, Cinhal, EMBASE, AIDSLINE, HealthSTAR, CANCERLIT, the Cochrane Library (clinical trials registry and the Database of Systematic Reviews), Micromedex, and Federal Research in Progress databases and references of reviewed articles. Included articles were written in English and dealt with randomized placebo-controlled trials of antidepressant medication use among adults with chronic back pain. Two reviewers abstracted data independently. Two continuous outcomes, change in back pain severity and ability to perform activities of daily living, were measured. Study quality was assessed with the methods used by Jadad and colleagues, and data were synthesized using a random-effects model. RESULTS Nine randomized controlled trials with 10 treatment arms and 504 patients were included. Seven treatment arms included patients with major depression. Patients had chronic back pain, averaging 10.4 years. Patients treated with antidepressants were more likely to improve in pain severity than those taking placebo (standardized mean difference, 0.41; 95% confidence interval, 0.22-0.61) but not in activities of daily living (standardized mean difference, 0.24; 95% confidence interval, -0.21-0.69). Patients treated with antidepressants experienced more adverse effects (22% vs 14%, P =.01) than those receiving placebo. CONCLUSION Antidepressants are more effective than placebo in reducing pain severity but not functional status in chronic back pain.
Dissemination of invasive Salmonella via bacterial-induced extrusion of mucosal epithelia

Salmonella enterica is an intracellular bacterial pathogen that resides and proliferates within a membrane-bound vacuole in epithelial cells of the gut and gallbladder. Although essential to disease, how Salmonella escapes from its intracellular niche and spreads to secondary cells within the same host, or to a new host, is not known. Here, we demonstrate that a subpopulation of Salmonella hyperreplicating in the cytosol of epithelial cells serves as a reservoir for dissemination. These bacteria are transcriptionally distinct from intravacuolar Salmonella. They are induced for the invasion-associated type III secretion system and possess flagella; hence, they are primed for invasion. Epithelial cells laden with these cytosolic bacteria are extruded out of the monolayer, releasing invasion-primed and -competent Salmonella into the lumen. This extrusion mechanism is morphologically similar to the process of cell shedding required for turnover of the intestinal epithelium. In contrast to the homeostatic mechanism, however, bacterial-induced extrusion is accompanied by an inflammatory cell death characterized by caspase-1 activation and the apical release of IL-18, an important cytokine regulator of gut inflammation. Although epithelial extrusion is obviously beneficial to Salmonella for completion of its life cycle, it also provides a mechanistic explanation for the mucosal inflammation that is triggered during Salmonella infection of the gastrointestinal and biliary tracts.
Exploration of a PIM Design Configuration for Energy-Efficient Task Offloading

Processing in memory (PIM) has been proposed to overcome the structural difficulties associated with conventional types of computing architecture and to realize a breakthrough for applications with high data requirements. There have been numerous attempts to utilize the PIM concept. Among them, PIM offloading takes advantage of high memory bandwidths, and various sophisticated conditions have been proposed to offload certain jobs to PIM on an instruction, task or application basis. However, schemes thus far are complicated and difficult to use. This can hinder the widespread use of PIM. Moreover, a performance improvement is not guaranteed in all cases even with these complicated schemes. This paper focuses on the energy efficiency of PIM technology. The potential-based conditions are defined to offload as many tasks as possible. This is justified in that PIM takes absolute advantage over the host in terms of power consumption. A PIM configuration favorable to the selected tasks is then devised. Simulation results show that the combination of potential-based task selection and the associated design configuration can effectively speed up the process while also reducing the energy use in most cases.
Alpha-amanitin-insensitive transcription of variant surface glycoprotein genes provides further evidence for discontinuous transcription in trypanosomes.

Many, if not all, mRNAs in T.brucei start with the same sequence of 35 nucleotides, separately encoded in clustered so-called mini-exon repeats. From these mini-exon repeats a 141-nt precursor RNA with the 35-nt sequence at its 5' end is transcribed. Indirect evidence suggests that this RNA is linked in a second step to pre-mRNA transcripts. We have studied the sensitivity of RNA synthesis to alpha-amanitin in isolated trypanosome nuclei. Transcription of several protein coding genes is almost completely inhibited by a concentration of 5 micrograms alpha-amanitin per ml, whereas strong inhibition of mini-exon transcription is achieved with 200 micrograms alpha-amanitin per ml. In contrast, transcription of genes for variant surface glycoproteins (VSGs) is not inhibited by 1000 micrograms alpha-amanitin per ml, as is transcription of the genes for the major rRNAs. Since the mature VSG mRNAs start with the 35-nt sequence, our results provide additional evidence that the 35-nt sequence and the main part of VSG mRNA are produced from independent transcription units, these are transcribed by (partly) different RNA polymerases.
Unsupervised End-to-end Learning for Deformable Medical Image Registration

We propose a registration algorithm for 2D CT/MRI medical images with a new unsupervised end-to-end strategy using convolutional neural networks. The contributions of our algorithm are threefold: (1) We transplant traditional image registration algorithms to an end-to-end convolutional neural network framework, while maintaining the unsupervised nature of image registration problems. The image-to-image integrated framework can simultaneously learn both image features and transformation matrix for registration. (2) Training with additional data without any label can further improve the registration performance by approximately 10 %. (3) The registration speed is 100x faster than traditional methods. The proposed network is easy to implement and can be trained efficiently. Experiments demonstrate that our system achieves state-of-the-art results on 2D brain registration and achieves comparable results on 2D liver registration. It can be extended to register other organs beyond liver and brain such as kidney, lung, and heart.
Kocuria Flava Induced Growth and Chromium Accumulation in Cicer Arietinum L

In the present investigation a chromate tolerant rhizobacterium Kocuria flava was isolated and inoculated to the Cicer arietinum L to evaluate its effects on growth and chromium accumulation upon exposure of different concentration of chromium (1–10 μg ml−1) as Cr (VI) for 24 d. K. flava inoculated plant of C. arietinum demonstrated luxuriant growth as compared to non inoculated plant at respective concentration of Cr (VI). K. flava found to ameliorate chromium induced phytotoxicity in terms of chlorophylls, carotenoid and protein contents and thus helps the plant in acquiring higher biomass with high chromium concentration. After 24 d, maximum concentration of chromium recorded in root of C. arietinum (4892.39 μg g−1dw) inoculated with K. flava as compared to non inoculated plant (1762.22 μg g−1dw) upon exposure of 5 μg ml−1Cr (VI). Therefore, application of C. arietinum in association with K. flava could be more efficient in decontamination of chromium polluted site. Moreover, K. flava may be used as a bioresource for developing microbes assisted phytoremediation system due to its compatibility.
Coping with Chronic Low Back Pain: An Idiographic Exploration through Focus Groups

Objective: This article explores the coping construct held by individuals with chronic low back pain. The research addresses two criteria identified as important for coping research: it looks at people's appraisals and responses to the specific stressor of living with chronic low back pain, and it seeks to identify what these individuals actually think and do in response to the ongoing stressor of living with chronic pain. Method: Fifteen people with chronic low back pain who responded to a media release participated in focus group discussions on coping with chronic pain. Results: Analysis indicated the desirability, if not need, for a somatic focus, the reliance on higher order cognitive strategies for planful action, and the use of a varied repertoire of coping strategies. Conclusions: These findings are discussed both in terms of adjustment to chronic illness and in relation to current pain management practices.
Parcerias estratégicas flexíveis : concepção e fundamentos da teoria

Temos como objetivo principal neste artigo-ensaio debater a questao da retomada da importância, tanto no setor privado como no publico, da administracao estrategica e do planejamento estrategico. Pressupomos que existe a necessidade da adocao de novos parâmetros na definicao da estrategia para a tomada de decisao, em decorrencia das mudancas de paradigmas no mundo. Essas transformacoes estao provocando alteracoes profundas, de forma generalizada nos campos politico, socioeconomico, tecnologico, ambiental e cultural. A partir da revisao bibliografica do planejamento estrategico e da administracao estrategica, formulamos a concepcao e os fundamentos basicos da teoria denominada “parceria estrategica flexivel”, orientada para permitir a tomada de decisoes que conduzam a concretizacao de parcerias consistentes entre Estados-nacao, instituicoes nacionais e multilaterais, organizacoes e empresas publicas e privadas complexas. Concluimos que, a parceria estrategica flexivel se aplica as condicoes reais e instaveis do cenario mundial contemporâneo, onde acordos e projetos, antes de serem firmados pelos decisores, necessitam ser analisados de forma consistente, coerente e racional de modo a permitir que os objetivos almejados sejam alcancados.
Helicobacter bilis sp. nov., a novel Helicobacter species isolated from bile, livers, and intestines of aged, inbred mice

A fusiform bacterium with 3 to 14 multiple bipolar sheathed flagella and periplasmic fibers wrapped around the cell was isolated from the liver, bile, and lower intestine of aged, inbred mice. The bacteria grew at 37 and 42 degrees C under microaerophilic conditions, rapidly hydrolyzed urea, were catalase and oxidase positive, reduced nitrate to nitrite, did not hydrolyze indoxyl acetate or hippurate, and were resistant to both cephalothin and nalidixic acid but sensitive to metronidazole. On the basis of 16S rRNA gene sequence analysis, the organism was classified as a novel helicobacter, Helicobacter bilis. This new helicobacter, like Helicobacter hepaticus, colonizes the bile, liver, and intestine of mice. Although the organism is associated with multifocal chronic hepatitis, further studies are required to ascertain whether H. bilis is responsible for causing chronic hepatitis and/or hepatocellular tumors in mice.
Emergence of OXA-48 and OXA-181 Carbapenemases among Enterobacteriaceae in South Africa and Evidence of In Vivo Selection of Colistin Resistance as a Consequence of Selective Decontamination of the Gastrointestinal Tract

ABSTRACT This study reports on the emergence of OXA-48-like carbapenemases among isolates of Enterobacteriaceae in South Africa. In addition, the emergence during therapy of a colistin-resistant OXA-181-producing Klebsiella pneumoniae isolate was documented following selective digestive tract decontamination with oral colistin, which is therefore strongly discouraged.
Design of a 80 Gbit/s SiGe BiCMOS fully differential input buffer for serial electrical communication

This paper presents a high bandwidth trans-impedance amplifier (TIA) used as a high speed input buffer for next generation serial electrical communication. The input buffer presented in this work is a linear broadband low noise amplifier. It is demonstrated that it can be used for receiving baseband modulated electrical communication in different modulation formats (NRZ, PAM4, duobinary, .) for bit rates up to 80 Gbit/s. With good impedance matching up to 50 GHz, an area of 0.18mm2 and a power consumption of 80mW from a 2.5V power supply.
Simultaneous metabolic labeling of cells with multiple amino acids: Localization and dynamics of histone acetylation and methylation

Simultaneous metabolic labeling of cells with multiple amino acids combined with acetic acid urea‐PAGE and MS was used to characterize histones in Kasumi‐1 cells treated with the histone deacetylase inhibitor depsipeptide (DDP). The approach allowed for rapid targeting, identification, and subsequent characterization of peptides containing sites of acetylation or methylation. Multiple methylation sites were determined for histone H3 including: di‐ and tri‐methylation of K9 and K27; mono‐ and di‐methylation of K36 and K79; and mono‐methylation of K37. The acetylation patterns for histones H4 and H3 were established. Quantitative analysis of the modification change after treatment with DDP was also performed and the dynamics of H4 acetylation determined. Functional analysis by RT‐PCR showed that DDP unregulated p21 expression with a maximum after 18‐h exposure. Chromatin immunoprecipitation experiments indicated that DDP treatment caused an accumulation of hyperacetylated histone H4 and H3 isoforms and a decrease in K9 di‐methylation of H3 on the p21 promoter.
Estimating The Eective Dimension Of High-Dimensional Finance Problems Using Sobol' Sensitivity Indices

Problems in many disciplines, such as physics, chemistry, and finance, can be modelled as integrals of high dimensions (hundreds or even thousands). Quasi-Monte Carlo (QMC) methods, which perform sampling using a more uniform point set than that used in MC, have been successfully used to approximate multivariate integrals with an error bound of size O((logN)kN−1) or even O((logN)kN−3/2), where N is the size of the sample and k depends on the dimension of the problem. This suggests an outperformance over the standard MC whose error bound is only O(N−1/2). But for high dimensional problems, this outperfomance might not appear at feasible sample sizes due to the dependence of the QMC convergence rate on the dimension of the problem. However, around 1993, it was found by researchers at Columbia University that QMC provides better convergence rates than MC for very high-dimensional problems in finance and in physics as well. This may be explained by the fact that the integrands in these problems have low “effective dimension” properties that interact positively with the properties of the point set used by the QMC method. To understand the efficiency of QMC, this paper uses Sobol’ method for global sensitivity analysis to investigate features of specific finance problems, digital option pricing and mortgage-backed securities, in dimensions as high as 360. Using Sobol’ sequences, we estimate the low-order Sobol’ sensitivity indices of these problems and estimate their effective dimensions accordingly. We also examine the efficiency of the Brownian Bridge technique in reducing the estimated effective dimension.
C + + Design Patterns for Managing Parameters in Scientific Computing

A scientific computing module usually has many parameters to control its behaviors. Instantiating a pair of get/set functions for each parameter clutters the interface, incurs code-bloating, overburdens maintenance, and invites subtle bugs. To solve these problems, two patterns are proposed for parameter management. The “enumeration index” pattern is a simple solution for parameters of a single type. When the parameters belong to multiple types, it is difficult for a statically-typed language to access/modify these parameters using a single pair of get/set functions. The “parameter manager” pattern achieves this by templates and multiple inheritance. It also handles additional semantics such as constancy, dependency, and default values in an easy-to-use manner: a client only has to specify the set of parameters and their associated properties. Both patterns are illustrated by a common task of solving the diffusion equation in the C++ language.
Endoscopic dilation of esophageal strictures.

OBJECTIVE To review the experience of endoscopic dilation of esophageal strictures at a tertiary care hospital. DESIGN Descriptive study. PLACE AND DURATION OF STUDY Shifa International Hospital, Islamabad January 1985 to January 2003. MATERIALS AND METHODS Patients presenting with dysphagia who presented at our institution during the past 8 years were reviewed. Their etiology and the number of dilations required for improvement in dysphagia and follow up with any complications were reviewed. All procedures were performed with savary dilators using guide wire without fluoroscopy. RESULTS A total of 369 patients were seen during this period and 583 procedures were performed. Two hundred thirty-five (63.7%) patients had peptic stricture, 123 (33.3%) had malignant strictures, 08 (2.2%) had non obstructive dysphagia and 6 (1.6%) had corrosive ingestions. The age ranged from 28-68 years. There were 254 (88.5%) males and 115 (31.2%) females. Sixty-seven (11.5%) procedures were performed as inpatient and 516 (88.5%) procedures were done as outpatient. Two to three attempts at dilatation were required to achieve satisfactory swallowing. There were no serious complication. Follow-up period was 6-8 weeks on an average. CONCLUSION Most common esophageal stricture found in our practice were peptic strictures. Dilation with savary system was safe and effective and was able to relieve dysphagia in large number of patients. No fluoroscopic guidance was needed.
PLGA-Alendronate Conjugate as a New Biomaterial to Produce Osteotropic Drug Nanocarriers

Targeting bone tissue to treat specific diseases, such as primary tumour or bone metastases from peripheral malignancies is a current and pressing research field for modern pharmaceutical technology, and nanomedicine in particular. Bone is the third most common site of metastasis and the incidence of bone metastases in patients died of cancer is reported to be around 70% [1,2]. Primary carcinomas of the lung, breast, prostate, kidney, and thyroid may develop skeletal metastases. In children affected by disseminated neuroblastoma bone metastases are also highly frequent. Tumour osteolysis is responsible for pathologic fractures, intractable pain, nerve compression syndrome, and severe hypercalcemia. In addition, patients with bone metastases may have neurologic impairment from spinal lesions, anaemia, and complications exacerbated by immobilization. Bone matrix resorption is minimally due to direct cancer cell activity. In fact, bone-colonizing tumour cells also stimulate osteoclastmediated bone resorption via the secretion of potent osteolytic agents [3]. The increased bone resorption that follows releases bone-derived growth factors into the extracellular milieu and systemic circulation, thereby further enhancing bone resorption, promoting tumour growth, and altering the tumour microenvironment. Vice versa, metastatic cancer cells are largely influenced by messages embedded within the bone matrix [4]. Under the influence of bone microenvironment, tumour cells proliferate and interact with osteoblasts and osteoclasts leading to lytic or sclerotic lesions. Clinical management of metastatic bone disease is really hard. The probability of long-term survival decreases dramatically in patients with skeletal metastases. Current treatments are based both on systemic therapy (chemotherapy, immunotherapy, hormone therapy) [5,6] and local therapy (surgery and radiotherapy) [7,8]. The restoration of functionality and mobility, along with pain relief can improve patients’ quality of life, but is unable to affect the negative progression of the disease. Because of the unique characteristics of tumours growth within bone tissues, conventional therapeutic strategies often lack efficiency in cure bone metastases. Moreover, most of the drugs used for the adjuvant therapy of osteolytic metastases interfere with signalling that induce osteoclast differentiation and osteoclast-mediated bone resorption, but they are not effective on tumour growth in the bone and their use is obviously associated with heavy side effects.