Miracle-dz/UniFAR-FTUs huggingface dataset:
VH replacement in primary immunoglobulin repertoire diversification

Significance The recombinatorial process of V(D)J rearrangement generates a vast antibody repertoire from a limited number of genes. The joints generated in the course of V(D)J recombination are imprecise thus yielding greater diversity but also resulting in frequent generation of nonproductive VDJ rearrangements. We have previously shown that B cells with two nonproductive IgH rearrangements can be efficiently rescued by a form of secondary V(D)J recombination called VH replacement. We now demonstrate that VH replacement also contributes to the diversity of the immune repertoire by modifying productive IgH rearrangements. Results presented herein suggest that VH replacement occurs exclusively during early stages of B-cell development and therefore does not contribute to the editing of self-reactive antibodies. The genes encoding the variable (V) region of the B-cell antigen receptor (BCR) are assembled from V, D (diversity), and J (joining) elements through a RAG-mediated recombination process that relies on the recognition of recombination signal sequences (RSSs) flanking the individual elements. Secondary V(D)J rearrangement modifies the original Ig rearrangement if a nonproductive original joint is formed, as a response to inappropriate signaling from a self-reactive BCR, or as part of a stochastic mechanism to further diversify the Ig repertoire. VH replacement represents a RAG-mediated secondary rearrangement in which an upstream VH element recombines with a rearranged VHDHJH joint to generate a new BCR specificity. The rearrangement occurs between the cryptic RSS of the original VH element and the conventional RSS of the invading VH gene, leaving behind a footprint of up to five base pairs (bps) of the original VH gene that is often further obscured by exonuclease activity and N-nucleotide addition. We have previously demonstrated that VH replacement can efficiently rescue the development of B cells that have acquired two nonproductive heavy chain (IgH) rearrangements. Here we describe a novel knock-in mouse model in which the prerearranged IgH locus resembles an endogenously rearranged productive VHDHJH allele. Using this mouse model, we characterized the role of VH replacement in the diversification of the primary Ig repertoire through the modification of productive VHDHJH rearrangements. Our results indicate that VH replacement occurs before Ig light chain rearrangement and thus is not involved in the editing of self-reactive antibodies.
Cane molasses and cottonseed meal supplementation of ammoniated tropical grass hay for yearling cattle.

Laboratory, digestion, and growth studies were used to evaluate liquid cane molasses (MOL) and(or) cottonseed meal (CSM) supplementation of ammoniated (4% of the forage DM) stargrass (Cynodon nlemfuensis Vanderyst var. nlemfuensis) hay. Ammoniation increased (P < .01) total N concentration (1.0 to 1.4% vs 1.7 to 2.8%) and in vitro digestion of OM, NDF, and ADF and decreased (P < .01) NDF concentration of stargrass hay. Two digestion (4 x 4 Latin square, 250-kg steers) and two growth (230-kg Brahman crossbred steers, seven to eight steers per pasture, three to four pastures per treatment, October through February) trials evaluated MOL and(or) CSM supplementation of ammoniated hay. Supplementation with CSM alone did not influence (P > .05) apparent digestibilities of OM or NDF, whereas supplementation with MOL either alone or with CSM increased (P < .05) apparent OM digestibility, but decreased (P < .05) apparent NDF digestibility. In the growth trials, hay intake was not affected (P > .05) by supplementation with CSM alone and was decreased (P < .05) by supplementation with MOL either alone or with CSM; however, total feed intake was increased (P < .05) by MOL supplementation. Cattle fed only ammoniated hay gained approximately . 20 kg/d. In both trials, daily gain and gain/feed were improved (P < .05) by CSM (.39 to .47 kg; .062 to .071) or MOL (.34 to .35 kg; .047 to .048) supplementation. Improvements (P < .05) in daily gain (.54 to .76 kg) and gain/feed (.077 to .083) by supplementation with MOL plus CSM were additive to responses from supplementation with MOL or CSM individually. (ABSTRACT TRUNCATED AT 250 WORDS)
Item recognition is less impaired than recall and associative recognition in a patient with selective hippocampal damage

This article explores the recall, item recognition, and associative recognition memory of patient B.E. , whose pattern of retrograde amnesia was reported by Kapur and Brooks ( 1999 ; Hippocampus 9:1–8). Structural magnetic resonance imaging (MRI) has shown that B.E. has bilateral damage restricted to the hippocampus. The structural damage he had sustained was accompanied by bilateral hypoperfusion of the temporal lobe, revealed by positron emission tomography (PET), and which single photon emission computed tomography (SPECT) suggested was greater in the left than the right temporal lobe. B.E. showed a global anterograde amnesia for verbal material, but he displayed some sparing of nonverbal item recognition relative to nonverbal recall and associative recognition. His performance on an item recognition task that used the remember/know procedure and another that involved repetition of the test phase, to reduce the difference between the familiarity of the targets and foils, suggested that his relatively spared nonverbal item recognition may have been mainly supported by familiarity. This finding is consistent with the view that the anterior temporal lobe, including the perirhinal cortex, can support familiarity‐based memory judgments (Brown and Bashir, 2002 ; Philos Trans R Soc Lond B 357:1083–1095). B.E. 's data also highlight the importance of functional as well as structural scan information for interpreting the pattern of memory deficits shown by patients with selective hippocampal structural lesions. © 2004 Wiley‐Liss, Inc.
Mass conservative three‐dimensional water tracer distribution from Markov chain Monte Carlo inversion of time‐lapse ground‐penetrating radar data

Time‐lapse geophysical measurements are widely used to monitor the movement of water and solutes through the subsurface. Yet commonly used deterministic least squares inversions typically suffer from relatively poor mass recovery, spread overestimation, and limited ability to appropriately estimate nonlinear model uncertainty. We describe herein a novel inversion methodology designed to reconstruct the three‐dimensional distribution of a tracer anomaly from geophysical data and provide consistent uncertainty estimates using Markov chain Monte Carlo simulation. Posterior sampling is made tractable by using a lower‐dimensional model space related both to the Legendre moments of the plume and to predefined morphological constraints. Benchmark results using cross‐hole ground‐penetrating radar travel times measurements during two synthetic water tracer application experiments involving increasingly complex plume geometries show that the proposed method not only conserves mass but also provides better estimates of plume morphology and posterior model uncertainty than deterministic inversion results.
Economic Fluctuations and Capitalistic Production: A Case Study in Robustness Constraints

A central pursuit of macroeconomic research is to understand the source of short run variations in aggregate economic variables. To this end, the branch of macroeconomics known as Real Business Cycle (RBC) theory emphasizes the role of disturbances to the real economy while abstracting from nominal variables (e.g. money). According to RBC theory, business cycles are the result of optimal responses to exogenous stochastic disturbances on technology in a structure of capitalistic production. In this report, we contend that the structure of capitalistic production per se constrains the ability of the economy to absorb shocks. That is, even if the feedback behavior in the model is designed to mitigate fluctuation (and is not necessarily optimal relative to some inter-temporal utility), the resulting sensitivity is nevertheless constrained by a lower bound. Moreover, we show that this lower bound is exacerbated with increasing steady state consumption, capital and investment. Concretely, we show that the Ramsey model, linearized about its steady state equilibrium, has a non-minimum phase structure and therefore its sensitivity is constrained by the control theoretic design limits. Moreover, the non-minimum phase zero is given by the inverse of the discount factor. As the discount factor approaches unity, steady state consumption approaches optimal steady state consumption, but the non-minimum phase zero approaches the closed unit circle exacerbating the sensitivity constraints.
Functional and Nutritional Characteristics of Cassava Flour (Lafun) Fortified with Soybeans

This study was designed for nutrition fortification of cassava flour lafun with soya beans. Five different samples of lafun to soya beans were (100:0, 90:10, 80:20, 70:30, and 60:40). The following proximate analysis of these samples were carried out ash determination, crude fiber, protein, moisture and fat. The results ranges were 0.84-2.46%, 1.63-2.12%, 1.16-12.54%, 13.01- 11.28% and 0.44-2.62% respectively. Functional properties of the formulation were also evaluated and the result obtained showed that loose and packed bulk density were 0.2-0.3% and 0.5- 0.55%, the water absorption and oil capacity were 163-127% and 167-113.5% respectively. Swelling capacity and disposability were also 6.2-2.95% and 93.7-81.4% while the regulation and solubility are 24.5-18.99 and 6.7-4.95 respectively. The pasting properties results were also revealed that at a peak of 244.17-112.33rvu, the trough was 129.17-58.83rvc,and the breakdown was 115.00-52.50rvu, the final viscosity was between 164.33-81.92rvu,set back 35.17-23.08rvu, peak time 4.46-3.91 and pasting temperature 63.15-63.850C. DOI: 10.5901/jesr.2013. v3n8p163
Contemporary Models of Youth Development and Problem Prevention: Toward an Integration of Terms, Concepts, and Models.

Over the past several years, increased interest in preventing youth problems and promoting healthy youth development has led youth and family practitioners, policy makers, and researchers to develop a wide range of approaches based on various theoretical frameworks. Although the growth in guiding frameworks has led to more complex models and a greater diversity in the options available to scholars and practitioners, the lack of an integrative conceptual scheme and consistent terminology has led to some confusion in the field. Here, we provide an overview of three approaches to youth development and problem prevention, critically examine their strengths and weaknesses, and offer some elaborations to help clarify, extend, and integrate the models. We conclude by discussing some general implications for researchers, practitioners, and policy makers. I n recent years, efforts to address youth problems and enhance youth development have become increasingly more broad-based, involving families, professionals, and community leaders representing a wide range of professions and constituencies. Family professionals are likely to be key players in these initiatives, given their interest in the wellbeing of youth and the important role that families play during adolescence. Paralleling this movement toward broad-based, community approaches to youth issues has been the growth of conceptual frameworks used to guide policy and programs aimed at preventing youth problems and enhancing development. Although this growth has led to more complex models and greater diversity in options available to scholars and practitioners, the lack of an integrative conceptual scheme and consistent terminology has fostered confusion in the field. Such issues are not unique to the field of youth development or to adolescence, but also are germane to family scholars interested in other periods of the life course as well. In this article, we briefly review the most prominent of these approaches, examine their origins, and highlight what we believe are their primary strengths and weaknesses. We then discuss how these approaches can be better integrated and expanded. We end by considering some implications for both theory and practice. Contemporary models of youth development and problem prevention generally can be grouped into one of three types: prevention, resiliency, and positive youth development. Although each approach makes a unique contribution to our understanding of coping, development, and human adaptation, they also share several key features and a mutual vision directed at improving the life chances of young people. Unfortunately, the literature in this area fails to provide consistency in the terminology used to designate certain fundamental constructs common to them all, especially with respect to terms related to risk and protection, assets or resources, and the designation of successful outcomes. For this reason, we begin with a brief discussion of terminology to provide a clearer understanding of our use of these terms.
Unsupervised Bug Report Categorization Using Clustering and Labeling Algorithm

Bug reports are one of the most crucial information sources for software engineering offering answers to many questions. Yet, getting these answers is not always easy; the information in bug reports is often implicit and some processes are required to extract the meaning of these reports. Most research in this area employ a supervised learning approach to classify bug reports so that required types of reports could be identified. However, this approach often requires an immense amount of time and effort, the resources that already too scarce in many projects. We aim to develop an automated framework that can categorize bug reports, according to their grammatical structure without the need for labeled data. Our framework categorizes bug reports according to their text similarity using topic modeling and a clustering algorithm. Each group of bug reports are labeled with our new clustering labeling algorithm specifically made for clusters in the topic space. Our framework is highly customizable with a modular approach and options to incorporate available background knowledge to improve its performance, while our cluster labeling approach make use of natural language process (NLP) chunking to create the representative labels. Our experiment results demonstrate that the performance of our unsupervised framework is comparable to a supervised learning one. We also show that our labeling process is capable of labeling each cluster with phrases that are representative for that cluster's characteristics. Our framework can be used to automatically categorize the incoming bug reports without any prior knowledge, as an automated labeling suggestion system or as a tool for obtaining knowledge about the structure of the bug report repository.
Serine Repeat Antigen (SERA5) Is Predominantly Expressed among the SERA Multigene Family of Plasmodium falciparum, and the Acquired Antibody Titers Correlate with Serum Inhibition of the Parasite Growth*

The Plasmodium falciparum serine repeat antigen (SERA) is one of the blood stage malaria vaccine candidates. The malaria genome project has revealed that SERA is a member of the SERA multigene family consisting of eight SERA homologues clustered on chromosome 2 and one SERA homologue on chromosome 9. Northern blotting and real time quantitative reverse transcription-PCR with five independent parasite strains, including three allelic representative forms of the SERA gene, have shown that all of the SERA homologues are transcribed most actively at trophozoite and schizont stages and that SERA5 (SERA/SERP) is transcribed predominantly among the family. Polyclonal antibodies were raised against recombinant proteins representing the N-terminal portions of four significantly transcribed SERA homologues (SERA3 to -6) in the center of the cluster on chromosome 2. Using these antibodies, indirect immunofluorescence microscopy detected the expression of SERA3 to -6, with similar localization, in all trophozoite- and schizont-infected erythrocytes. We have examined 40 sera from Ugandan adults for their antibody reactivity and found that enzyme-linked immunosorbent assay titer against SERA5 N-terminal domain, but not against other SERA proteins, is positively correlated with the inhibition of in vitro parasite growth by individual sera. Our data confirm the usefulness of the N-terminal domain of SERA5 as a promising malaria candidate vaccine.
Patterns of (18)F-FDG uptake in adipose tissue and muscle: a potential source of false-positives for PET.

UNLABELLED The routine use of PET/CT fusion imaging in a large oncology practice has led to the realization that (18)F-FDG uptake into normal fat and muscle can be a common source of potentially misleading false-positive PET imaging in the neck, thorax, and abdomen. The goal of this study was to characterize this normal variant of (18)F-FDG uptake in terms of incidence and characteristic extent. METHODS All body scans done on our PET/CT scanners in July and August 2002 were retrospectively reviewed. All cases in which increased (18)F-FDG uptake in the neck was not localized to lymph nodes or other obvious anatomic sites on the CT scans were included in this study. Sites of any unexplained (18)F-FDG uptake in the rest of the body were also recorded. RESULTS A total of 863 PET scans (476 males, 387 females; age, 2-88 y; mean age, 57 y) were reviewed. The following distinctive patterns of nonpathologic (18)F-FDG activity were observed: (a) neck fat, 20 patients (2.3%); (b) paravertebral uptake, 12 patients (1.4%); (c) perinephric fat, 7 patients (0.8%); (d) mediastinal fat, 8 patients (0.9%); (e) normal musculature, 12 patients (1.4%). Patients showing paravertebral uptake, perinephric fat, and mediastinal fat were all associated with the neck fat pattern, singly or in combination. On the other hand, patients showing the normal musculature pattern did not show any of the other uptake. In this analysis, the incidence of (18)F-FDG uptake in sites other than the neck is restricted to the patient population with neck fat uptake and may be an underestimation of the true incidence. Neck fat is found predominantly in females, whereas normal musculature is usually seen in males (P < 0.01, Fisher exact test). Neck fat is also seen significantly more in the pediatric population (4/26 = 15%) than in the adult population (16/837 = 1.9%) (P < 0.01, Fisher exact test). CONCLUSION Increased (18)F-FDG uptake is sometimes seen in individual muscles and in adipose tissue in the neck and shoulder region, axillae, mediastinum, and perinephric regions. There is also associated (18)F-FDG uptake in the intercostal spaces in the paravertebral regions. (18)F-FDG uptake in neck fat is more commonly seen in female patients and the pediatric population. The pattern of uptake as well as the age and sex distribution suggest that the (18)F-FDG in fat is in the brown adipose tissue. It is important to recognize this uptake pattern to avoid false interpretation of this benign normal variant as a malignant finding on (18)F-FDG PET scans.
Modafinil: A gift to portmanteau

This article reviews the use of modafinil in palliative care, and its use in promoting vigilance and wakefulness. Modafinil’s therapeutic and chemical class, mechanism of action, pharmacokinetics, indications, dosage, side effects, and drug interactions are also discussed. Modafinil seems to fit the requirements of portmanteau, using one drug to treat multiple symptoms.
Mechanism of Action of Inhalational Anesthesia on Airways

To separate reflex from direct actions of anesthetics on airways, we studied the effects of halothane and isoflurane (1.5 MAC) on Ascaris antigen-induced (a mixed reflex and direct stimulus) and methacholine-induced (a direct acting stimulus) airway constriction in Basenji-Greyhound dogs. Prior to aerosol challenge, pulmonary resistance (RL) and dynamic compliance (Cdyn) were not different during control (thiopental), halothane, and isoflurane anesthesia. RL was 1.93 · 0.15 (mean · SE), 1.81 · 0.23 and 2.1 cm 0.12 cm H2. l−1.s during thiopental, halothane, and isoflurane, respectively. Cdyn was 116 · 8, 106 · 16 and 110 · 9 ml/cmH3O during thiopental, halothane, and isoflurane anesthesia, respectively. In control studies (thiopental), Ascaris antigen increased RL by 9·4 · 2.44 fold and decreased Cdyn to 0.29 · . 02 times the prechallenge value. Both halothane and isoflurane anesthesia significantly attenuated the increase in RL provoked by Ascaris antigen challenge and halothane significantly attenuated the decrease in Cdyn. During halothane and isoflurane anesthesia, Ascaris antigen increased RL by 3.8 · 0.96 and 3.5 · 0.57 fold, respectively, and decreased Cdyn to 0.48 · 0.09 and 0.38 · . 07 times the prechallenge value, respectively. In control studies (thiopental anesthesia), methacholine produced dose-related increases in RL and decreases in Cdyn. Both halothane and isoflurane attenuated the increase in RL and the decrease in Ccyn provoked by methacholine with halothane being more effective than isoflurane with regards to Cdyn. The mechanism of action of halothane and isoflurane on airways is similar and complex, involving depression of airway reflexes as well as direct effects on airway smooth muscle.
Current utilization of breast FNA in a cytology practice

Over the past decade, core biopsy rapidly replaced fine needle aspiration (FNA) in evaluation of diseases of the female breast in many centers in the USA. The inability to diagnose invasive cancer by FNA, and the general feeling of unease in interpretation of cytologic specimens among pathologists who are not trained in cytopathology are among factors leading to decline in the use of FNA. At our institution, we continue to rely heavily on FNA for evaluation of breast masses. In this article, we discuss our multidisciplinary team approach which is essential in sustaining a successful breast cancer screening program. We also review the general utility of breast FNA and core biopsy in a comparative fashion. In the second part of this article which will appear in an upcoming issue, we will review the use of FNA and core biopsy in challenging breast lesions focusing on the pitfalls and limitations of both modalities in selected specific lesions. Diagn. Cytopathol. 2009. © 2008 Wiley‐Liss, Inc.