Miracle-dz/UniFAR-FTUs huggingface dataset:
Breath tests in the diagnosis of small intestinal bacterial overgrowth in patients with irritable bowel syndrome in comparison with quantitative upper gut aspirate culture

Background Small intestinal bacterial overgrowth (SIBO) is reported in 4–78% patients with irritable bowel syndrome (IBS). This wide range of percentages might be because of the different techniques and criteria used to define the condition. We studied the utility of early (breath hydrogen increase 20 ppm above basal within 90 min) and double peaks on lactulose and glucose hydrogen breath tests (LHBT and GHBT, respectively) to diagnose SIBO (gold standard: upper gut aspirate culture). We also studied the clinical parameters that are associated with SIBO among them. Methods Overall, 80 patients with IBS (Rome 3) were evaluated for SIBO using aspirate culture, GHBT, and LHBT (with methane). Results A total of 15/80 (19%) patients had SIBO (≥105 CFU/ml) on culture compared with 0/10 historical controls; 4/15 (27%) with and none of 65 without SIBO had positive GHBT (sensitivity 27%, specificity 100%). None of 15 with and one of 65 without SIBO had double peaks on LHBT (sensitivity 0%, specificity 98%); 5/15 (33%) with and 23/65 (35%) without SIBO had an early peak on LHBT (sensitivity 33%, specificity 65%); and 2/15 (13.3%) with and 26/63 (41.3%) without SIBO had high methane on LHBT (sensitivity 13.3%, specificity 58.7%). Patients with SIBO on culture more often had diarrhea [6/15 (40%) vs. 8/65 (12.3%), P=0.011], higher weekly stool frequency [21 (3–28) vs. 14 (4–49), P=0.003], and looser forms [Bristol 5–6, 11/15 (73.3%) vs. 33/65 (50.8%), P=0.116]. Conclusion On the basis of culture, 19% patients with IBS had SIBO. The specificity of GHBT was 100%, but the sensitivity of this test and the diagnostic performances of LHBT and breath methane were all very poor. SIBO was more common in IBS patients with diarrhea than in patients with other bowel habits.
Sea level from temperature profiles in the tropical Pacific Ocean

We investigate how well the 1975-1992 sea level interannual variability in the tropical Pacific is captured by dynamic height from temperature profiles. For each temperature profile, a surface dynamic height relative to 300 m is estimated, assuming a constant temperature-salinity relationship. After multiplication by a latitudinally varying factor and the removal of a seasonal cycle, the dynamic height deviations fit the tide gauge sea level variability to within the sampling errors, except at a few sites near the equator west of the date line, where surface salinity variability is large. The dynamic height data are assimilated into a wind-forced linear numerical model of the sea level in the tropical Pacific, applying a Kaitaart filter in a space of reduced dimension. A limited number of empirical orthogonal functions of the unfiltered run (1975-1992) define the reduced space, into which the Kalman Filter covariance evolution calculation is done (Cane et al., 1996). Experiments indicate that results are better with 32 functions than with a smaller number but are not improved by retaining more functions. The resulting analyzed fields of sea level are compared to withheld dynamic height estimates from moorings, sea level data from tide gauges, and sea level analyses made with the same Kaitaart filter fommlism applied to tide gauge measemenm. The comparisons to observations suggest that the temperature profries were usually sufficient to constrain the monthly analyzed fields to be close to the observed sea level with errors typically less than 3 cm near the equator. The comparison to tide gauge sea level reveals that this analysis is often more accurate than the analysis of tide gauge sea level data with which it shares many characteristics. Near the equator west of the date line, salinity variations are large and their neglect in estimating dynamic height has a negative impact on the analysis. The analyzed signal is underestimated in the southwest Pacific and at more than 20 o off the equator. The reanalysis of the temperature data done with a primitive equation model at the National Meteorological Center (NMC) (Ji et al., 1995; Enfield and Harris, 1995) does not share this problem. On the other hand, NMC reanalysis (14) departs more from the observations elsewhere, although more data were included than in our analysis.
An Evaluation of Maes's Bottom-Up Mechanism for Behavior Selection

Maes has proposed a mechanism for action selection (behavioral choice) (Maes, 1989, 1990, 1991 a), which is reviewed here and is evaluated using a simulated environment. This simulated environment is a detailed and complex generalized model of the action selection problem faced by an animal in the wild and presents a rather severe test for an action selection mechanism. The results of testing Maes's mechanism in the simulated environment are discussed, some observed deficiencies in the mechanism's operation are described, and the computational reasons underlying the deficiencies are explained. lt is argued that some central aspects of the design of Maes's mechanism mean that it is not able to deal well with animal like action selection problems.
Detection of ROS1 rearrangement in non-small cell lung cancer: current and future perspectives

ROS1 rearrangement characterizes a small subset (1%–2%) of non-small cell lung cancer and is associated with slight/never smoking patients and adenocarcinoma histology. Identification of ROS1 rearrangement is mandatory to permit targeted therapy with specific inhibitors, demonstrating a significantly better survival when compared with conventional chemotherapy. Detection of ROS1 rearrangement is based on in situ (immunohistochemistry, fluorescence in situ hybridization) and extractive non-in situ assays. While fluorescence in situ hybridization still represents the gold standard in clinical trials, this technique may fail to recognize rearrangements of ROS1 with some gene fusion partner. On the other hand, immunohistochemistry is the most cost-effective screening technique, but it seems to be characterized by low specificity. Extractive molecular assays are expensive and laborious methods, but they specifically recognize almost all ROS1 fusions using a limited amount of mRNA even from formalin-fixed, paraffin-embedded tumor tissues. This review is a discussion on the present and futuristic diagnostic scenario of ROS1 identification in lung cancer.
Incremental garbage collection for causal relationship computation in distributed systems

Many distributed applications require the knowledge of the causality relation induced by the computation. Reconstructing this relation appears to be an interesting tool for such applications, but a vector of size S - where S is the number of processes - must be attached to each event to achieve this reconstruction. This induces a large overhead in secondary memory. After defining special events of the computation - some kind of checkpoints - we propose two algorithms that discard unnecessary data for the causal relationship reconstruction. The first algorithm acts on-the-fly while the second acts during reconstruction. <<ETX>>
Dawn Phenomenon and Somogyi Effect in IDDM

We examined the clinical relevance of a rise in fasting blood glucose (BG) between 0300 and 0600 in 97 patients with insulin-dependent diabetes mellitus (IDDM) receiving sequentially conventional (CT) and basal-bolus (BBIT) insulin therapies and assessed the impact of one potential causal factor, i.e., posthypoglycemic hyperglycemia, with 231 BG profiles (97 during CT, 134 during BBIT) in which BG was measured every 3 h over a 24-h period. A rise in BG between 0300 and 0600 occurred in 157 of 231 (68%) profiles. The mean magnitude of this rise was 56 ±39 mg/dl and was lower (P < .05) during BBIT (48 ± 35 mg/dl, n = 97) than CT (62±43 mg/dl, n = 97). A dawn rise (between 0300 and 0600) >50 mg/dl occurred in 40 of 97 (41%) profiles during CT and 26 of 97 (27%) during BBIT (P < .05). When all profiles were grouped according to the magnitude of this rise in BG, the mean daytime BG (from 0900 to 1800) was higher (P < .05) after an 0300–0600 BG rise >50 mg/dl compared with groups of profiles showing either a fall in BG or a rise <50 mg/dl; a rise in BG between 0300 and 0600 correlated (r = .38, P < .0001) with the subsequent mean daytime BG. Nocturnal hypoglycemia (BG <60 mg/dl) recorded at 2400 and/or 0300 occurred in 57 of 231 (25%) profiles. After nocturnal hypoglycemia, the highest BG recorded before breakfast was only 215 mg/dl, and the mean BG at 0600 was considerably lower (P < .0001) in profiles showing at least one episode of nocturnal hypoglycemia (116 ± 45 mg/dl, n = 57) compared with all profiles in which no nocturnal hypoglycemia was detected (174 ± 85 mg/dl, n = 174). In addition, postbreakfast BG levels at 0900 were lower (P < .0001) after nocturnal hypoglycemia (171 ± 87 mg/dl, n = 57) than when no nocturnal hypoglycemia was detected (211 ± 91 mg/dl, n = 174). We conclude that a dawn rise in BG commonly occurs in IDDM patients receiving either CT or BBIT. A dawn BG rise >50 mg/dl may lead to significant exacerbation of daytime hyperglycemia. Nocturnal hypoglycemia does not contribute to morning hyperglycemia, but conversion from CT to BBIT can achieve a modest reduction in the frequency and magnitude of an early-morning rise in BG.
Repression of the Human Sex Hormone-binding Globulin Gene in Sertoli Cells by Upstream Stimulatory Transcription Factors*

Expression of the sex hormone-binding globulin gene (SHBG) in the liver produces SHBG, which transports sex steroids in the blood. In rodents, the SHBG gene is also expressed in Sertoli cells giving rise to the testicular androgen-binding protein, which is secreted into the seminiferous tubule where it presumably controls testosterone action. Evidence that the SHBG gene functions in this way in the human testis is lacking, and mice containing a human SHBG transgene (shbg4) under the control of its own promoter sequence are characterized by SHBG gene expression in the liver but not in the testis. A potential cis-element, defined as footprint 4 (FP4) within the human SHBG promoter, is absent in SHBG promoters of mammals that produce the testicular androgen-binding protein, and we have produced mice harboring a shbg4 transgene in which FP4 was deleted to evaluate its functional significance. Remarkably, these mice express the modified human SHBG transgene in the testis as well as the liver. Human SHBG transcripts were found within their Sertoli cells, primary cultures of which secrete human SHBG, and this was increased by treatment with follicle-stimulating hormone, retinoic acid, and estradiol but not testosterone. We have also found that the upstream stimulatory factors (USF-1 and USF-2) bind FP4 in vitro by electromobility shift assay of Sertoli cell nuclear extracts and in vivo by chromatin immunoprecipitation assay and conclude that USF transcription factors repress human SHBG transcription in Sertoli cells through an interaction with FP4 within its proximal promoter.
Occupational exposure to electromagnetic fields and acute leukaemia: analysis of a case-control study

Aims: To investigate whether the risk of acute leukaemia among adults is associated with occupational exposure to electromagnetic fields. Methods: Probable occupational exposure to electromagnetic fields at higher than typical residential levels was investigated among 764 patients diagnosed with acute leukaemia during 1991–96 and 1510 sex and age matched controls. A job exposure matrix was applied to the self reported employment histories to determine whether or not a subject was exposed to electromagnetic fields. Risks were assessed using conditional logistic regression for a matched analysis. Results: Study subjects considered probably ever exposed to electromagnetic fields at work were not at increased risk of acute leukaemia compared to those considered never exposed. Generally, no associations were observed on stratification by sex, leukaemia subtype, number of years since exposure stopped, or occupation; there was no evidence of a dose-response effect using increasing number of years exposed. However, relative to women considered never exposed, a significant excess of acute lymphoblastic leukaemia was observed among women probably exposed to electromagnetic fields at work that remained increased irrespective of time prior to diagnosis or job ever held. Conclusion: This large population based case-control study found little evidence to support an association between occupational exposure to electromagnetic fields and acute leukaemia. While an excess of acute lymphoblastic leukaemia among women was observed, it is unlikely that occupational exposure to electromagnetic fields was responsible, given that increased risks remained during periods when exposure above background levels was improbable.
The current state of resident training in genomic pathology: a comprehensive analysis using the resident in-service examination.

OBJECTIVES To determine the current state of pathology resident training in genomic and molecular pathology. METHODS The Training Residents in Genomics (TRIG) Working Group developed survey and knowledge questions for the 2013 pathology Resident In-Service Examination (RISE). Sixteen demographic questions related to amount of training, current and predicted future use, and perceived ability in molecular pathology vs genomic medicine were included, along with five genomic pathology and 19 molecular pathology knowledge questions. RESULTS A total of 2,506 pathology residents took the 2013 RISE, with approximately 600 individuals per postgraduate year (PGY). For genomic medicine, 42% of PGY-4 respondents stated they had no training, compared with 7% for molecular pathology (P < .001). PGY-4 residents' perceived ability, comfort in discussing results, and predicted future use as a practicing pathologist were reported to be less in genomic medicine than in molecular pathology (P < .001). Based on PGY, knowledge question scores showed a greater increase in molecular pathology than in genomic pathology. CONCLUSIONS The RISE is a powerful tool for assessing the state of resident training in genomic pathology and current results suggest a significant deficit. The results also provide a baseline to assess future initiatives to improve genomics education for pathology residents such as those developed by the TRIG Working Group.
Measuring molecular information.

Although information theory was developed more than 50 years ago (Shannon, 1948, 1949), it is widely accepted (Gappmair, 1999), and a complete compendium of Claude Shannon's works was recently published (Sloane & Wyner, 1993). The application of information theory to understanding binding sites of proteins on DNA or RNA was published more than 10 years ago (Schneider et al., 1986), and since then it has been pro"tably used to study many genetic systems (see http:// www .lecb. ncifcrf .gov /&toms/ ). Shannon measured information as an average property of signals passing through a communications channel, so a natural extension is to understand the information contributed by individual symbols. The same extension can be applied to the study of binding sites as an &&individual information theory'' (Schneider, 1997a, b) and this has also been successfully used to understand a variety of genetic and medically relevant systems (Hengen et al., 1997; Rogan et al., 1998; Allikmets et al., 1998; Kahn et al., 1998; Shltzaberger & Schneider, 1999; Zheng et al., 1999). Dr Stormo subsequently published a letter in this journal promoting an alternative to the Shannon approach and pointed out some consequences of that choice (Stormo, 1998). In this letter I will address other consequences and interpretations of the two approaches. However, before addressing the deep and di$cult issues that Dr Stormo has raised, which we have been discussing for more than 15 years, I would like to make some small factual corrections. First, the Staden method (Staden, 1984) is discussed in my J. theor. Biol. paper (Schneider, 1997a). Staden's method has no cuto! , while the individual information (R i ) method has a natural one and although they are similar, no one derived
Foraging habitat and diet of Song Sparrows (Melospiza melodia) nesting in farmland: a stable isotope approach

Agricultural intensification has been linked to declines in farmland and grassland bird populations in Europe and in North America. One factor thought to be behind these declines is reduced invertebrate food abundance in the breeding season, leading to reduced reproductive success. However, little is known about foraging habitat or diet of farmland birds in North America. We used stable isotopes to study foraging habitat and diet of Song Sparrows (Melospiza melodia (A. Wilson, 1810)), a common hedgerow-breeding bird, by collecting claw clippings of Song Sparrow nestlings from farms in eastern Ontario, Canada. Mean values of 13 C and 15 N were compared between claws and invertebrate food sources from adjacent land-cover types, using a Bayesian mixing model. The portion of nestling diet that came from seminatural and forage habitats was higher than expected, based on the proportion of seminatural and forage cover at the nest. This was particularly evident at nests with low seminatural cover, where hedgerows were the only noncrop habitat. The most important food sources for Song Sparrow nestlings were hoppers (Auchenorrhyncha) and caterpillars (Lepidoptera). Management actions to increase invertebrate abundance in hedgerows may benefit Song Sparrows and other farmland birds with minimal impact on crop yield.
Quantitation of blood‐brain barrier defect by magnetic resonance imaging and gadolinium‐DTPA in patients with multiple sclerosis and brain tumors

In this study quantitation of the degree of deficiency of the blood‐brain barrier (BBB) in patients with multiple sclerosis or brain tumors, by using MRI, is shown to be possible. As a measure of permeability of the BBB to Gadolinium‐DTPA (Gd‐DTPA) the flux per unit of distribution volume per unit of brain mass was used. This quantity was found by introducing the longitudinal relaxation rate (R1) as a measure of concentration of Gd‐DTPA in the brain tissue in the mathematical model for the transcapillary transport over the BBB. High accordance between the observed data points and the model was found, and the results were comparable to results obtained from similar studies using positron emission tomography. The improved possibility of quantitating the defect of the BBB by MRI may give new information about pathogenesis or etiology, and leads to improved methods in monitoring the efficacy of treatments in intracranial diseases. © 1990 Academic Press, Inc.
Pricing currency options in the Heston/CIR double exponential jump-diffusion model

We examine currency options in the double exponential jump-diffusion version of the Heston stochastic volatility model for the exchange rate. We assume, in addition, that the domestic and foreign stochastic interest rates are governed by the CIR dynamics. The instantaneous volatility is correlated with the dynamics of the exchange rate return, whereas the domestic and foreign short-term rates are assumed to be independent of the dynamics of the exchange rate and its volatility. The main result furnishes a semi-analytical formula for the price of the European currency call option in the hybrid foreign exchange/interest rates model.
Facial point detection based on ASMS learning from 3D models

Detecting a set of facial points is a crucial phase for facial expression analysis and face recognition, yet the robust facial point detector is yet to be developed. In this paper we present a method based on Active Shape Model of Subsets (ASMS) learning from 3D models to drastically reduce the time needed to search for a point's location and increase the accuracy and robustness of the algorithm. Using 3D Information allows us to expand training samples and set up complete point distribution models (PDMs). On the other hand, training samples are grouped into different subsets, which makes detection of the points very fast and the algorithm robust to pose and illumination variations as well. In order to improve the accuracy of location, objective function and parameter optimization process of Active Appearance Model (AAM) will be introduced in ASMS. The proposed point detection algorithm was tested on WHU-3D-2D database, the results of which showed we outperform current state of the art point detectors.
The open-open topology for function spaces

Let (X,T) and (Y,T*) be topological spaces and let F⊂YX. For each U∈T, V∈T*, let (U,V)={f∈F:f(U)⊂V}. Define the set S∘∘={(U,V):U∈T and V∈T*}. Then S∘∘ is a subbasis for a topology, T∘∘ on F, which is called the open-open topology. We compare T∘∘ with other topologies and discuss its properties. We also show that T∘∘, on H(X), the collection of all self-homeomorphisms on X, is equivalent to the topology induced on H(X) by the Pervin quasi-uniformity on X.
Linear Precoder Design for SWIPT in MIMO Broadcasting Systems With Discrete Input Signals: Manifold Optimization Approach

In this paper, we investigate the design of linear precoders for simultaneously wireless information and power transfer (SWIPT) in a multi-input multi-output (MIMO) broadcasting system with discrete input signals. The considered system model consists of one base station (BS), one information receiver (IR), and one energy receiver (ER). The design objective is to maximize the input–output mutual information of the IR subject to the power constraint and the harvested energy requirement for the ER. We derive the structure of the optimal linear precoder by using manifold optimization, and propose an algorithm to find the optimal precoder. Simulation results show that the proposed algorithm can achieve better performance than the time sharing scheme and the Gaussian optimal precoder when Gaussian inputs are replaced by discrete input signals.
Hypertension and end‐organ damage in pediatric renal transplantation

Abstract: The prevalence of hypertension in pediatric patients with renal transplant (Tx) has not changed for the last three decades, remaining at 50–80%. Long‐standing and uncontrolled hypertension is associated with the development of end‐organ damage including allograft dysfunction, early cardiomyopathy and premature atherosclerosis. Aggressive treatment of elevated BP is an essential part of Tx care with the goal to delay graft failure and prevent the development of symptomatic cardiovascular disease in young recipients of renal Tx.
Dakota Commemorative March: Thoughts and Reactions

For the past ten years I have been an associate professor in Indigenous Studies and Dakota Studies (inds) at Southwest State University (ssu). At the 8th Annual inds Spring Conference in April 2001, the first planning discussion occurred concerning a march to honor the Dakota women and children who were on the forced march in November 1862. We had a number of planning meetings for the Dakota Commemorative March at ssu. On the march I served as one of the Minnesota contact persons and as a “gofer”: “go fer” this and “go fer” that. One of the Dakota communities, located at Santee, Nebraska, donated a buffalo. This provided about eight hundred pounds of meat. So, I delivered one hundred-pound chunks of meat to the various communities that cooked and fed the marchers. The marchers who participated in the Commemorative March 140 years after the 1862 event came from South Dakota and North Dakota, Dakota Commemorative March