Miracle-dz/UniFAR-FTUs huggingface dataset:
Malabsorption syndrome with and without small intestinal bacterial overgrowth: A study on upper‐gut aspirate using 1H NMR spectroscopy

Biochemicals in the upper‐gut aspirate in 31 patients with malabsorption syndrome (MAS) with and without small intestinal bacterial overgrowth (SIBO), and 10 disease‐free controls were analyzed using high‐resolution 1H‐NMR spectroscopy, and were correlated with the degree of SIBO and severity of MAS. Compared to controls, the patients had higher quantities (μmol/L: median [range]) of total bile acids/cholesterol (2000 [0–12000] vs. 300 [0–600]), lactate (700 [0–5200] vs. nil [0–30]), acetate (200 [0–6500] vs. 20 [0–200]), and formate (80 [0–900] vs. nil [0–50]) (P < 0.01, Mann‐Whitney U‐test). However, amino acids and glucose were comparable in both. Quantities (μmol/L: median [range]) of acetate (1330 [220–6500] vs. 100 [0–1430]), lactate (1430 [670–3300] vs. 300 [0–5200]), formate (360 [0–600] vs. 25 [0–800]), and unconjugated bile acids (500 [40–600] vs. 10 [0–300]) were higher in MAS patients with SIBO than those without SIBO (P < 0.01, Mann‐Whitney U‐test, for all). In patients with MAS the quantity of acetate positively correlated with the degree of SIBO, and unconjugated bile acids correlated with the degree of steatorrhoea (Spearman's rank correlation coefficient, two‐tailed, P < 0.05: 0.46 and 0.52, respectively). This study demonstrates the bacterial production of metabolites and deconjugation of bile acids in patients with MAS. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Stakeholder initiatives in flood risk management: exploring the role and impact of bottom-up initiatives in three ‘Room for the River’ projects in the Netherlands

In recent years stakeholder participation has become a popular topic in flood management. Little is known about how and under which circumstances local stakeholders initiate and develop successful flood management strategies and how governmental actors respond to them. Drawing on theories of social movements, stakeholder participation, and citizenship, this paper analyses how local stakeholder initiatives in the Dutch ‘Room for the River’ programme evolve and, in turn, influence such governmental plans and actions. The description and comparative analysis of the three cases leads to three conclusions: first, in all cases, forms of local self-organization play a role, but its impacts are highly dependent on the mix of strategies chosen. Second, forms of coproduction between local stakeholders and government actors are the most viable strategy to realize the positive impact of local initiatives. Third, government agencies tend to react to local initiatives defensively. Much depends on timing and connecting to the right people.
High-Velocity Microsprays Enhance Antimicrobial Activity in Streptococcus mutans Biofilms

Streptococcus mutans in dental plaque biofilms play a role in caries development. The biofilm’s complex structure enhances the resistance to antimicrobial agents by limiting the transport of active agents inside the biofilm. The authors assessed the ability of high-velocity water microsprays to enhance delivery of antimicrobials into 3-d-old S. mutans biofilms. Biofilms were exposed to a 90° or 30° impact, first using a 1-µm tracer bead solution (109 beads/mL) and, second, a 0.2% chlorhexidine (CHX) or 0.085% cetylpyridinium chloride (CPC) solution. For comparison, a 30-s diffusive transport and simulated mouthwash were also performed. Confocal microscopy was used to determine number and relative bead penetration depth into the biofilm. Assessment of antimicrobial penetration was determined by calculating the killing depth detected by live/dead viability staining. The authors first demonstrated that the microspray was able to deliver significantly more microbeads deeper in the biofilm compared with diffusion and mouthwashing exposures. Next, these experiments revealed that the microspray yielded better antimicrobial penetration evidenced by deeper killing inside the biofilm and a wider killing zone around the zone of clearance than diffusion alone. Interestingly the 30° impact in the distal position delivered approximately 16 times more microbeads and yielded approximately 20% more bacteria killing (for both CHX and CPC) than the 90° impact. These data suggest that high-velocity water microsprays can be used as an effective mechanism to deliver microparticles and antimicrobials inside S. mutans biofilms. High shear stresses generated at the biofilm-burst interface might have enhanced bead and antimicrobial delivery inside the remaining biofilm by combining forced advection into the biofilm matrix and physical restructuring of the biofilm itself. Further, the impact angle has potential to be optimized both for biofilm removal and active agents’ delivery inside biofilm in those protected areas where some biofilm might remain.
Fast ultrasound imaging simulation in K-space

Most available ultrasound imaging simulation methods are based on the spatial impulse response approach. The execution speed of such a simulation is of the order of days for one heart-sized frame using desktop computers. For some applications, the accuracy of such rigorous simulation approaches is not necessary. This work outlines a much faster 3-D ultrasound imaging simulation approach that can be applied to tasks like simulating 3-D ultrasound images for speckle-tracking. The increased speed of the proposed simulation method is based primarily on the approximation that the point spread function is set to be spatially invariant, which is a reasonably good approximation when using polar coordinates for simulating images from phased arrays with constant aperture. Ultrasound images are found as the convolution of the PSF and an object of sparsely distributed scatterers. The scatterers are passed through an anti-aliasing filter before insertion into a regular beam-space grid to reduce the bandwidth and significantly reduce the amount of data. A comparison with the well-established simulation software package field II has been made. A simulation of a cyst image using the same input object was found to be in the order of 7000 times slower than the presented method. Following these considerations, the proposed simulation method can be a rapid and valuable tool for working with 3-D ultrasound imaging and in particular 3-D speckle-tracking.
On the rank one abelian Gross-Stark conjecture

Let $F$ be a totally real number field, $p$ a rational prime, and $\chi$ a finite order totally odd abelian character of Gal$(\bar{F}/F)$ such that $\chi(\mathfrak{p})=1$ for some $\mathfrak{p}|p$. Motivated by a conjecture of Stark, Gross conjectured a relation between the derivative of the $p$-adic $L$-function associated to $\chi$ at its exceptional zero and the $\mathfrak{p}$-adic logarithm of a $p$-unit in the $\chi$ component of $F_\chi^\times$. In a recent work, Dasgupta, Darmon, and Pollack have proven this conjecture assuming two conditions: that Leopoldt's conjecture holds for $F$ and $p$, and that if there is only one prime of $F$ lying above $p$, a certain relation holds between the $\mathscr{L}$-invariants of $\chi$ and $\chi^{-1}$. The main result of this paper removes both of these conditions, thus giving an unconditional proof of the conjecture.
15q overgrowth syndrome: A newly recognized phenotype associated with overgrowth, learning difficulties, characteristic facial appearance, renal anomalies and increased dosage of distal chromosome 15q

Trisomy and tetrasomy of distal chromosome 15q have rarely been reported. Although most of the described patients have some learning difficulties and are overgrown, the phenotype associated with distal trisomy/tetrasomy 15q is uncertain due to the small numbers of reported cases and the common co‐occurrence of additional chromosome deletions in many patients with trisomy 15q. We present five individuals with overgrowth, learning difficulties and increased dosage of distal 15q. Partial trisomy 15q was identified in four of these cases. Two were generated through recombination of a parental pericentric inversion and two were generated through malsegregation of a maternal balanced 14;15 reciprocal translocation. In all four cases the trisomy can be considered “pure” as the 14p and 15p monosomies will exert no phenotypic effect. Partial tetrasomy 15q, as the result of an analphoid supernumerary chromosome derived from an inverted duplication of distal 15q, was identified in the fifth patient. In addition to the overgrowth and learning difficulties, all five had a characteristic facial appearance and three had renal anomalies. The gestalt consists of a long, thin face with a prominent chin and nose. Renal anomalies included renal agenesis, horseshoe kidney, and hydronephrosis. We provide further support for a distinct “15q overgrowth syndrome” caused by either trisomy or tetrasomy resulting in increased dosage of distal 15q. In addition we propose that renal anomalies and a distinctive facial appearance be considered major features of this condition. © 2009 Wiley‐Liss, Inc.
Validation of a PCR-Based Method for Detection of Food-Borne Thermotolerant Campylobacters in a Multicenter Collaborative Trial

ABSTRACT A PCR-based method for rapid detection of food-borne thermotolerant campylobacters was evaluated through a collaborative trial with 12 laboratories testing spiked carcass rinse samples. The method showed an interlaboratory diagnostic sensitivity of 96.7% and a diagnostic specificity of 100% for chicken samples, while these values were 94.2 and 83.3%, respectively, for pig samples.
Cyclooxygenase‐2 gene promoter polymorphisms affect susceptibility to hepatitis C virus infection and disease progression

Aim: Because polymorphisms of cyclooxygenase‐2 (COX‐2) and osteopontin (OPN) promoter regions and a promoter/enhancer region of forkhead box protein 3 (FOXP3) gene are known to affect immune responses, we examined whether these polymorphisms can influence susceptibility to hepatitis C virus (HCV) infection and progression of liver disease.
Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes.

PURPOSE To analyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. METHODS Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index) Calculator. RESULTS Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position) composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs), translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX) genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. CONCLUSIONS Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.
L-amphetamine improves memory in MS patients with objective memory impairment

Background: Memory impairment is prevalent in multiple sclerosis (MS), but no drugs are approved to treat these memory problems. Objective: The objective of the study was to examine the effect of l-amphetamine versus placebo on auditory/verbal memory and visual/spatial memory in MS patients with and without baseline memory impairment. Methods: We conducted a re-analysis of a previously published clinical trial in which MS patients were randomly assigned to treatment (30 mg l-amphetamine, N = 99) or placebo (N = 37) in a four-week, double-blind, parallel-group, dose titration trial. Auditory/verbal memory (CVLT-II: Long Delay Free Recall) and visual/spatial memory (BVMT-R: Delayed Recall) were assessed at baseline and follow-up across subgroups of patients with intact baseline memory (mean = 50th percentile) or impaired baseline memory (mean = 2nd percentile). Primary analyses: 2 (l-amphetamine, placebo) × 2 (baseline, follow-up), × 2 (baseline memory intact, baseline memory impaired) ANOVAs performed separately for auditory/verbal and visual/spatial memory. Results: For both auditory/verbal and visual/spatial memory, we observed significant 2 × 2 × 2 interactions whereby l-amphetamine improved memory more than placebo, and this effect was specific to patients with baseline memory impairment. Conclusions: Among memory-impaired patients, memory improved about 48.5% for those on l-amphetamine, but only 1.0% on placebo. Treatment with l-amphetamine produced large memory gains among memory-impaired MS patients.
In Vivo Fluoroscopic Analysis Of Fixed-Bearing Total Knee Replacements

In vivo kinematic patterns were determined for subjects (patients participating in the study), having either a fixed-bearing posterior-stabilized or posterior cruciate-retaining total knee arthroplasty. While under fluoroscopic surveillance, subjects did normal gait and a deep knee bend. Video images were downloaded to a workstation computer and analyzed in three dimensions using an iterative model-fitting approach. Femorotibial contact paths for the medial and lateral condyles, axial rotation, and condylar lift-off were determined. During a deep knee bend, subjects having a posterior-stabilized total knee arthroplasty routinely experienced posterior femoral rollback of their lateral condyle and normal axial rotational patterns, whereas random subjects having a posterior cruciate-retaining total knee arthroplasty experienced paradoxical anterior sliding and opposite axial rotational patterns. During gait, posterior-stabilized and posterior cruciate-retaining total knee arthroplasties experienced similar kinematic patterns, with the presence of paradoxical sliding and opposite axial rotational patterns. Subjects having posterior-stabilized and posterior cruciate-retaining total knee arthroplasties experienced condylar lift-off. Subjects having a posterior cruciate-retaining total knee arthroplasty predominantly experienced lateral condylar lift-off whereas subjects with posterior-stabilized total knee arthroplasties experienced either medial or lateral condylar lift-off. Subjects having a posterior-stabilized total knee arthroplasty experienced significantly greater weightbearing range of motion.
Chromosome aberrations in a series of 120 multiple myeloma cases with abnormal karyotypes

We identified 120 multiple myeloma (MM) cases with satisfactory cytogenetic evaluation and abnormal karyotypes. Hyperdiploid karyotype was found in 77 cases (64%), hypodiploid in 30 cases (25%), and the remaining 13 cases (11%) had a pseudodiploid karyotype. The most common numerical abnormalities were gains of chromosomes 15, 9, 3 followed by chromosomes 19, 11, 7, 21, and 5. Whole chromosome losses were also frequent involving primarily chromosomes X/Y, 8, 13, 14, and 22. Most cases showed also structural rearrangements leading to del(1p), dup(1q), del(5q), del(6q), del(8p), del(9p), del(13q), and del(17p). Chromosome 13/13q deletion was found in 52% of cases; complete loss of 13 was observed in 73% of cases, whereas 27% had interstitial deletions. In addition, 13/13q deletions occurred in 75% of nonhyperdiploid myeloma but only 39% of the hyperdiploid had 13/13q deletions. Translocations affecting 14q32/IGH region was seen 40 cases; t(11;14)(q13;q32) in 17 cases, t(14;16)(q32;q23) and t(8;14)(q24;q32) in three cases each, and t(6;14)(p21;q32) and t(1;14)(q21;q32) in two cases each. The remaining 14q32 translocations had various t(V;14) partners or of an undetermined origin. Remarkably, the 14q32/IGH translocations were less frequent in the hyperdiploid karyotypes than the nonhyperdiploid karyotypes (17 vs. 63%). Fourteen cases showed break at 8q24/CMYC site; seven of those had Burkitt's‐type translocations. Our results revealed that conventional cytogenetics remains an important tool in elucidating the complex and divers genetic anomalies of MM. Cytogenetics identifies two distinct groups of MM, hyperdiploid and nonhyperdiploid, and establishes the presence of prognostic chromosomal markers such as 13/13q, 17p, 8q24, and 16q aberrations. Am. J. Hematol. , 2007. © 2007 Wiley‐Liss, Inc.
Effectiveness of Food Subsidies in Raising Healthy Food Consumption: Public Distribution of Pulses in India

&NA; This paper provides evidence on the effectiveness of one of the most common policies to improve nutrition among the poor, that is, a food subsidy. We study the case of subsidies on pulses in select Indian states and their impact on consumption and ultimately nutrition (protein intake). As a natural experiment, we use the introduction of pulses into India's Public Distribution System (PDS) where the variations in prices were brought about by the inclusion of pulses in the PDS in some states and not in others. Our difference in difference (DID) estimates show that change in the consumption of pulses because of their inclusion in the PDS, though statistically significant, was of a small order. The impact was not large enough to bring about any sizable difference in consumption of pulses or the total protein intake. The results withstand several robustness checks including randomized inference and triple differencing based on location and other consumer characteristics.
Interleukin‐10 rescues T cells from apoptotic cell death: association with an upregulation of Bcl‐2

We demonstrate that interleukin‐10 (IL‐10) can inhibit T‐cell apoptosis. T cells, within a PBMC (peripheral blood mononuclear cell) population, were stimulated via the T‐cell receptor and grown in the presence of IL‐2. These cells had less apoptosis when in the continuous presence of IL‐10, compared with cells grown in the absence of IL–10. Conversely, when stimulated and grown in the presence of neutralizing antibody to IL‐10, there was an increase in T‐cell apoptosis. The in vitro rescue from apoptotic cell death of other lymphoid cells, such as germinal centre B cells, has been shown by others to involve a Bcl‐2 pathway. We therefore investigated whether IL‐10 might affect the Bcl‐2 expression on cultured T cells. By Western blotting we demonstrated that continuous exposure of IL‐10 to T cells (within a PBMC population) enhanced the expression of Bcl‐2. Furthermore, T cells protected from apoptotic cell death by IL‐10 were indistinguishable from viable untreated cells in their ability to proliferate to either immobilized anti‐CD3 or IL‐2. Thus, we have shown that continuous culture of T cells in the presence of IL‐10 will inhibit T‐cell apoptosis because of, at least in part, the upregulation of Bcl‐2, and this is associated with a normal proliferative function.
CRH functions as a growth factor/cytokine in the skin

We tested the effect of CRH and related peptides in a large panel of human skin cells for growth factor/cytokine activities. In skin cells CRH action is mediated by CRH‐R1, a subject to posttranslational modification with expression of alternatively spliced isoforms. Activation of CRH‐R1 induced generation of both cAMP and IP3 in the majority of epidermal and dermal cells (except for normal keratinocytes and one melanoma line), indicating cell type‐dependent coupling to signal transduction pathways. Phenotypic effects on cell proliferation were however dependent on both cell type and nutrition conditions. Specifically, CRH stimulated dermal fibroblasts proliferation, by increasing transition from G1/0 to the S phase, while in keratinocytes CRH inhibited cell proliferation. In normal and immortalized melanocytes CRH effect showed dichotomy and thus, it inhibited melanocyte proliferation in serum‐containing medium CRH through G2 arrest, while serum free media led instead to CRH enhanced DNA synthesis (through increased transition from G1/G0 to S phase and decreased subG1 signal, indicating DNA degradation). CRH also induced inhibition of early and late apoptosis in the same cells, demonstrated by analysis with the annexin V stains. Thus, CRH acts on epidermal melanocytes as a survival factor under the stress of starvation (anti‐apoptotic) as well as inhibitor of growth factors induced cell proliferation. In conclusion, CRH and related peptides can couple CRH‐R1 to any of diverse signal transduction pathways; they also regulate cell viability and proliferation in cell type and growth condition‐dependent manners. J.Cell. Physiol. © 2005 Wiley‐Liss, Inc.
Deficiency of essential GTP‐binding protein ObgE in Escherichia coli inhibits chromosome partition

GTP‐binding proteins are involved in cell proliferation, development, signal transduction, protein elongation, etc. and construct the GTPase superfamily, whose structures and sequence motifs (G‐1 to G‐5) are highly conserved from prokaryote to eukaryote. Obg of Bacillus subtilis and Obg homologues of other bacteria belong to the GTPase superfamily and have been suggested as being essential for cell growth, development and monitoring of intracellular levels of GTP. We identified the Obg homologue in Escherichia coli, a protein previously known as YhbZ, which we have renamed ObgE. Double cross‐over experiments showed that the obgE gene is essential for growth in E. coli. From characterization of the obgE temperature‐sensitive mutant, we found that DNA replication was not inhibited, that the nucleoids did not partition and instead remained in the middle of cell, and that the cells elongated. Overproduction of ObgE also resulted in aberrant chromosome segregation. These data suggested that ObgE is involved directly or indirectly in E. coli chromosome partitioning. Characterization studies showed that ObgE is abundant in normal cells, partially associated with the membrane and does not associate with ribosomes such as in Obg of B. subtilis. We purified ObgE protein from a cell extract of E. coli, and the purified ObgE had GTPase activity and DNA‐binding ability.
Bilateral Intravenous Regional Anesthesia: A New Method to Test Additives to Local Anesthetic Solutions

Background Ketorolac, when added to lidocaine, has been shown to reduce early tourniquet pain during intravenous regional anesthesia (IVRA) in patients. Although the effectiveness of ropivacaine 0.2% for IVRA is equal to that of lidocaine 0.5% but significantly reduces central nervous system side effects after release of the tourniquet, it provides no advantage with regard to tourniquet tolerance times. Simultaneous bilateral IVRA with ropivacaine 0.2% was used to test the hypothesis that ketorolac modifies tourniquet tolerance and to test whether drug combinations can be evaluated in one study session. Methods Ten healthy, unsedated volunteers received 30 ml of ropivacaine 0.2% in each upper arm with 2 ml of normal saline in one arm and 30 mg of ketorolac in the contralateral arm for IVRA. Both proximal tourniquets remained inflated for 30 min, followed by inflation of the distal tourniquets and release of the proximal ones. Verbal numeric scores for tourniquet pain were recorded for both extremities. Central nervous system side effects were graded after release of each distal tourniquet. Results There was no difference between the two upper extremities with regard to surgical anesthesia and tourniquet tolerance. Total tourniquet tolerance was a median of 58.5 min (range, 45–90 min) and 60.5 min (39–79 min) in the normal saline and ketorolac groups, respectively. After release of the distal tourniquets, 5 of 10 volunteers experienced mild dizziness. Conclusions The addition of ketorolac to ropivacaine does not improve tourniquet tolerance. Minimal central nervous system side effects after tourniquet release suggest that a total of 60 ml ropivacaine 0.2% for bilateral IVRA is a useful model for comparison of IVRA drug combinations.