Miracle-dz/UniFAR-FTUs huggingface dataset:
Intestinal Oxalobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate.

BACKGROUND AND PURPOSE Oxalobacter formigenes is an anaerobic commensal colonic bacterium capable of degrading oxalate through the enzyme oxalyl-CoA decarboxylase. It has been theorized that individuals who lack this bacterium have higher intestinal oxalate absorption, leading to a higher urinary oxalate concentration and an increased risk of calcium oxalate urolithiasis. We performed a prospective, controlled study to evaluate O. formigenes colonization in calcium oxalate stone formers and to correlate colonization with urinary oxalate and other standard urinary stone risk factors. PATIENTS AND METHODS Thirty-five first-time calcium oxalate stone formers were compared with 10 control subjects having no history of urolithiasis and a normal renal ultrasound scan. All subjects underwent standard metabolic testing by submitting serum and 24-hour urine specimens. In addition, all subjects submitted stool samples for culture and detection of O. formigenes by Xentr(ix) O. formigenes Monitor. RESULTS Intestinal Oxalobacter was detected in only 26% of the stone formers compared with 60% of the controls (p < 0.05). Overall, the average urinary oxalate excretion by the two groups was similar (38.6 mg/day v 40.8 mg/day). Among stone formers, however, there were statistically higher urinary oxalate concentrations in O. formigenes-negative patients compared with those testing positive (41.7 mg/day v 29.4 mg/day) (p = 0.03). Furthermore, all 10 stone formers with hyperoxaluria (>44 mg/day) tested negative for O. formigenes (p < 0.05). CONCLUSIONS Calcium oxalate stone formers have a low rate of colonization with O. formigenes. Among stone formers, absence of intestinal Oxalobacter correlates with higher urinary oxalate concentration and an increased risk of hyperoxaluria. Introduction of the Oxalobacter bacterium or an analog of its enzyme oxalyl-CoA decarboxylase into the intestinal tract may be a treatment for calcium oxalate stone disease.
Preoperative chemotherapy followed by surgery compared with primary surgery in resectable stage I (except T1N0), II, and IIIa non-small-cell lung cancer.

PURPOSE To evaluate whether preoperative chemotherapy (PCT) could improve survival in resectable stage I (except T1N0), II, and IIIA non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS A randomized trial compared PCT to primary surgery (PRS). PCT consisted of two cycles of mitomycin (6 mg/m(2), day 1), ifosfamide (1.5 g/m(2), days 1 to 3) and cisplatin (30 mg/m(2), days 1 to 3), and two additional postoperative cycles for responding patients. In both arms, patients with pT3 or pN2 disease received thoracic radiotherapy. RESULTS Three hundred fifty-five eligible patients were randomized. Overall response to PCT was 64%. There were two preoperative toxic deaths. Postoperative mortality was 6.7% in the PCT arm and 4.5% in the PRS arm (P =.38). Median survival was 37 months (95% confidence interval [CI], 26.7 to 48.3) for PCT and 26.0 months (95% CI, 19.8 to 33.6) for PRS (P =.15). Survival differences between both arms increased from 3.8% (95% CI, 1.3% to 25.1%) at 1 year to 8.6% (95% CI, 2.64% to 24.4%) at 4 years. A quantitative interaction between N status and treatment was observed, with benefit confined to N0 to N1 disease (relative risk [RR], 0.68; 95% CI, 0.49 to 0.96; P =.027). After a nonsignificant excess of deaths during treatment, the effect of PCT was significantly favorable on survival (RR, 0.74; 95% CI, 0.56 to 0.99; P =.044). Disease-free survival time was significantly longer in the PCT arm (P =.033). CONCLUSION Although impressive differences in median, 3-year, and 4-year survival were observed, they were not statistically significant, except for stage I and II disease.
Sjögren's syndrome diagnosed in pregnancy: a case report.

BACKGROUND As in most other autoimmune diseases, Sjögren's syndrome is seen predominantly in women. Since the peak age is around the late reproductive and early postmenopausal period, the obstetric aspect has not been well studied. CASE A 28-years-old woman, pregnant for 22 weeks and 5 days, was admitted with worsening general status, skin lesions, arthralgias, and oral and ocular symptoms typical of Sjögren's syndrome. She underwent hemodialysis for renal insufficiency. To prevent autoantibody formation, progression of the disease, therapy with methyl prednisolone, 100 mg/d intravenously; cyclophosphamide, 500 mg/month in a single intravenous application; hemodialysis 3 times a week; and plasmapheresis 7 times was instituted. An 1,100-g, male infant at 27 weeks and 5 days was delivered by cesarean section because of premature preterm rupture of membranes and severe late decelerations on cardiotocography. The infant was discharged from the neonatal intensive care unit after 30 days, weighing 1,800 g. Postnatal echocardiographic examination of the infant revealed neither cardiac malformations nor arrhythmias. CONCLUSION Since the presence of autoantibodies against SS-A and SS-B are reported to accompany congenital heart block, the primary goal of therapy should be preventing this untoward effect of the disease. Close monitoring during pregnancy is mandatory to detect preeclampsia, intrauterine growth retardation and preterm labor.
Micronucleus-centromere assay in workers occupationally exposed to low level of benzene

Benzene is a well-known carcinogen that induces chromosomal instability, including chromosome aberration and aneuploidy. In order to assess aneugenic effect of low-level benzene, micronucleus-centromere assay using specific probes for chromosomes 7 and 9 was performed in workers occupationally exposed to low-dose benzene at a petroleum refinery. A micronucleus-centromere assay using a pan-centromeric probe was also performed to determine the origin of benzene-induced micronucleus (MN). Frequency of aneuploidy of chromosomes 7 and 9 was significantly higher among workers compared to the unexposed control group. Poisson regression analysis revealed that aneuploidy frequency of chromosome 7 or 9 was significantly associated with benzene level after adjusting for confounding variables such as age, smoking, alcohol intake, and duration of work (p = .042). Additionally, frequencies of MN and centromere-negative micronuclei (MNC—) were significantly higher in benzene-exposed workers compared to controls, while frequency of centromere-positive micronuclei (MNC+) was similar in both groups. In conclusion, aneuploidy of chromosomes 7 and 9 could be a useful biomarker to assess the effect of low-level benzene exposure, and benzene-induced MN originates from chromosome breaks rather than chromosome non-disjunction.
A randomized controlled trial of early dietary supply of long‐chain polyunsaturated fatty acids and mental development in term infants

The effects of dietary docosahexaenoic acid (DHA) supply during infancy on later cognitive development of healthy term infants were evaluated in a randomized clinical trial of infant formula milk supplemented with 0.35% DHA or with 0.36% DHA and 0.72% arachidonic acid (AA), or control formula which provided no DHA or AA. Fifty‐six 18‐month‐old children (26 male, 30 female) who were enrolled in the trial within the first 5 days of life and fed the assigned diet to 17 weeks of age were tested using the Bayley Scales of Infant Development, 2nd edition (BSID‐II) (Bayley 1993) at the Retina Foundation of the Southwest, Dallas, TX. These children had also been assessed at 4 months and 12 months of age for blood fatty‐acid composition, sweep visual evoked potential (VEP) acuity, and forced‐choice preferential looking (FPL) acuity (Birch et al. 1998). Supplementation of infant formula with DHA+AA was associated with a mean increase of 7 points on the Mental Development Index (MDI) of the BSID‐II. Both the cognitive and motor subscales of the MDI showed a significant developmental age advantage for DHA‐ and DHA+AA‐supplemented groups over the control group. While a similar trend was found for the language subscale, it did not reach statistical significance. Neither the Psychomotor Development Index nor the Behavior Rating Scale of the BSID‐II showed significant differences among diet groups, consistent with a specific advantage of DHA supplementation on mental development. Significant correlations between plasma and RBC‐DHA at 4 months of age but not at 12 months of age and MDI at 18 months of age suggest that early dietary supply of DHA was a major dietary determinant of improved performance on the MDI.
Viral IL-10 gene therapy inhibits TNF-alpha and IL-1 beta, not IL-6, in the newborn endotoxemic mouse.

INTRODUCTION Modulation of the inflammatory cascade within the liver of critically ill infants may improve the chance of survival. Using gene therapy, the authors hypothesized that augmented local production of the counter-regulatory cytokine viral interleukin-10 (IL-10) in vivo will modulate the critical cytokines in the inflammatory response. The purpose of the present study was to determine whether replication-defective adenovirus-mediated viral IL-10 (vIL-10) gene transfer and expression within the liver can achieve this goal in newborn mice. MATERIALS AND METHODS Four-week-old Balb/c mice were administered (intraperitoneally) 1 x 10(9) plaque-forming units (pfu) per milliliter of an adenovirus vector (E1a/b-deleted) than encodes the sv40 promoter and the BCRF1 cDNA, or of control vector dl434 that expresses no foreign gene. Forty-eight hours later the mice were challenged with 50 micrograms/kg of lipopolysaccharide (LPS) they were killed 1, 2, 6, or 24 hours later (six at each time point). Southern blot analysis was performed on genomic DNA isolated from the liver, lung, and kidney to assess gene transfer of BCRF1. Homogenized liver protein was analyzed for tumor necrosis factor-alpha (TNF-alpha), IL-1 beta, IL-6, and recombinant vIL-10. RESULTS Southern blot analysis confirmed successful gene transfer to the liver but not to the lung, kidney, or dl434-transduced liver in mice that received adenovectors. Viral IL-10 levels within the liver ranged from 14 to 18 ng/mL. In controls, TNF-alpha production was elevated at early time points, to 18,000 pg/mL, but decreased rapidly by 24 hours after LPS challenge. The TNF-alpha levels of animals treated with Ad5svBCRF1 were significantly lower than those of controls throughout the course of study (P < .0001). After the LPS challenge, hepatic IL-1 beta decreased, from a maximum of 800 pg/mL (2 hours) to 411 pg/mL (24 hours). Inhibition of IL-1 beta by vIL-10 occurred at 1 hour (P > .016) and 2 hours (P < .001) only. Hepatic production of IL-6 after LPS challenge ranged from 7 to 8,000 pg/mL in all groups and was not altered by vIL-10 gene therapy. CONCLUSION In vivo administration of adenovectors encoding BCRF1 to newborn mice results in efficient hepatic transduction and expression of recombinant vIL-10. The Kupffer cell response to LPS is suppressed with respect to TNF-alpha and IL-1 beta, but not IL-6. In vivo modulation of hepatic cytokine responses is achievable using gene products that mimic cellular cytokines. This is an effective model for the selective evaluation of therapeutic gene products for gene therapy of sepsis.
Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes : implications for phage evolution

A118 is a temperate phage isolated from Listeria monocytogenes. In this study, we report the entire nucleotide sequence and structural analysis of its 40 834 bp DNA. Electron microscopic and enzymatic analyses revealed that the A118 genome is a linear, circularly permuted, terminally redundant collection of double‐stranded DNA molecules. No evidence for cohesive ends or for a terminase recognition (pac) site could be obtained, suggesting that A118 viral DNA is packaged via a headful mechanism. Partial denaturation mapping of DNA cross‐linked to the tail shaft indicated that DNA packaging proceeds from left to right with respect to the arbitrary genomic map and the direction of genes necessary for lytic development. Seventy‐two open reading frames (ORFs) were identified on the A118 genome, which are apparently organized in a life cycle‐specific manner into at least three major transcriptional units. N‐terminal amino acid sequencing, bioinformatic analyses and functional characterizations enabled the assignment of possible functions to 26 ORFs, which included DNA packaging proteins, morphopoetic proteins, lysis components, lysogeny control‐associated functions and proteins necessary for DNA recombination, modification and replication. Comparative analysis of the A118 genome structure with other bacteriophages revealed local, but sometimes extensive, similarities to a number of phages spanning a broader phylogenetic range of various low G+C host bacteria, which implies relatively recent exchange of genes or genetic modules. We have also identified the A118 attachment site attP and the corresponding attB in Listeria monocytogenes, and show that site‐specific integration of the A118 prophage by the A118 integrase occurs into a host gene homologous to comK of Bacillus subtilis, an autoregulatory gene specifying the major competence transcription factor.
Fuzzy Induction in Dynamic User Profiling for Information Filtering

In this paper we investigate the role of the user profile in information filtering and we introduce a novel algorithm for learning the user profile based on user’s initial profile and on a queries’ interpretation using fuzzy generalization (Angryk and Petry 2003). Thousands of documents are usually retrieved by search engines for a given query during an information search on WWW. One way to prune irrelevant documents is to take advantage of the user’s implicit interests to filter the documents returned by the search engine, or to reformulate the query based on these interests. One of the common representations of the documents (and queries) in information retrieval is based on the vector hyperspace model (Salton and McGill 1993). We are using the expanded version of Salton’s vector space model introduced by Barbu and Simina (2003) for its effectiveness in computing the dynamics of the user profile. In contrast with the classical vector space model, this recent model, time-words vector hyperspace, has an additional temporal dimension. The coordinates of the documents and queries vectors are calculated using the traditional TF-IDF technique. Only the queries have a temporal dimension (current interest weight) which is set to a preset positive initial value that decays in time, suggesting that some specific user interests could decrease as time goes on. The user’s categories of interest are computed based on a novel approach using Fuzzy Concept Hierarchies (FCH) extracted from the WordNet ontology. An FCH is built for each of the query’s keywords, using their hypernym chains provided by WordNet. A subunitary membership degree (weight) is assigned for each of the edges of the hierarchy via a bottom-up approach, from the lowest level concept (initial keyword) to the more abstract one. The assignment of the weights is performed according to the following two conditions: 1) The sum of weights assigned to the links outgoing from the original keyword has to be equal to unity.
The Research Diagnostic Criteria for Temporomandibular Disorders. IV: evaluation of psychometric properties of the Axis II measures.

AIMS To evaluate the psychometric properties of the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) biobehavioral (Axis II) screening instruments. METHODS Participants with Axis I TMD diagnoses (n = 626) completed the Axis II instruments (Depression, Nonspecific Physical Symptoms, Graded Chronic Pain) and other instruments assessing psychological distress, pain, and disability at three study sites. Internal consistency, temporal stability, and convergent/discriminant validity of the Axis II measures were assessed. To assess criterion validity of Nonspecific Physical Symptoms and Depression instruments as screeners, 170 participants completed a structured psychiatric diagnostic interview. RESULTS The Axis II instruments showed very good to excellent internal consistency (Cronbach's alpha coefficients = 0.80 to 0.95). Their convergent (correlation range 0.3 to 0.9) and discriminant (range 0.0 to 0.6) validity were generally supported, although Nonspecific Physical Symptoms was more strongly associated with depressive than with somatic symptoms. Temporal stability was high for characteristic pain intensity (Lin's correlation concordance coefficient [CCC] = 0.91), interference (CCC = 0.89), and chronic pain grade (weighted kappa = 0.87), and fair to good for Depression and Nonspecific Physical Symptoms (CCC = 0.63 to 0.78). The Depression instrument normal versus moderate to severe cutoff point was good at identifying current-year depression and dysthymia diagnoses (sensitivity 87%, specificity 53%). Nonspecific Physical Symptoms did not have high utility for detecting psychiatric disorders (sensitivity 86%, specificity 31%). CONCLUSION The Axis-II Depression and Graded Chronic Pain instruments have clinically relevant and acceptable psychometric properties for reliability and validity and utility as instruments for identifying TMD patients with high levels of distress, pain, and disability that can interfere with treatment response and course of Axis I disorders.
Molecular and genetic analysis of a region of plasmid pCF10 containing positive control genes and structural genes encoding surface proteins involved in pheromone-inducible conjugation in Enterococcus faecalis

Exposure of Enterococcus faecalis cells carrying the tetracycline resistance plasmid pCF10 to the heptapeptide pheromone cCF10 results in an increase in conjugal transfer frequency by as much as 10(6)-fold. Pheromone-induced donor cells also express at least two plasmid-encoded surface proteins, the 130-kDa Sec 10 protein, which is involved in surface exclusion, and the 150-kDa Asc10 protein, which has been associated with the formation of mating aggregates. Previous subcloning and transposon mutagenesis studies indicated that the adjacent EcoRI c (7.5 kb) and e (4.5 kb) fragments of pCF10 encode the structural genes for these proteins and that the EcoRI c fragment also encodes at least two regulatory genes involved in activation of the expression of the genes encoding Asc10 and Sec10. In this paper, the results of physical and genetic analysis of this region of pCF10, along with the complete DNA sequences of the EcoRI c and e fragments, are reported. The results of the genetic studies indicate the location of the structural genes for the surface proteins and reveal important features of their transcription. In addition, we provide evidence here and in the accompanying paper (S. B. Olmsted, S.-M. Kao, L. J. van Putte, J. C. Gallo, and G. M. Dunny, J. Bacteriol. 173:7665-7672, 1991) for a role of Asc10 in mating aggregate formation. The data also reveal a complex positive control system that acts at distances of at least 3 to 6 kb to activate expression of Asc10. DNA sequence analysis presented here reveals the positions of a number of specific genes, termed prg (pheromone-responsive genes) in this region of pCF10. The genes mapped include prgA (encoding Sec10) and prgB (encoding Asc10), as well as four putative regulatory genes, prgX, -R, -S, and -T. Although the predicted amino acid sequences of Sec10 and Asc10 have some structural features in common with a number of surface proteins of gram-positive cocci, and the Asc10 sequence is highly similar to that of a similar protein encoded by the pheromone-inducible plasmid pAD1 (D. Galli, F. Lottspeich, and R. Wirth, Mol. Microbiol. 4:895-904, 1990), the regulatory genes show relatively little resemblance to any previously sequenced genes from either procaryotes or eucaryotes.
Comparison of Single-Visit and Multiple-Visit Measures of Retention in Care for HIV Monitoring and Evaluation.

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A Mobile Robotic Platform for Elderly Care

This paper presents the proposal of a robotic platform for elderly care integrated in the Living Usability Lab for Next Generation Networks. The project aims at developing technologies and services tailored to enable the active aging and independent living of the elderly population. The proposed robotic platform is based on the CAMBADA robotic soccer platform, with the necessary modifications, both at hardware and software levels, while simultaneously applying the experiences achieve in the robotic soccer environment.
Warming of Subarctic waters accelerates development of a key marine zooplankton Calanus finmarchicus

Recent observations confirm the rising temperatures of Atlantic waters transported into the Arctic Ocean via the West Spitsbergen Current (WSC). We studied the overall abundance and population structure of the North Atlantic keystone zooplankton copepod Calanus finmarchicus, which is the main prey for pelagic fish and some seabirds, in relation to selected environmental variables in this area between 2001 and 2011, when warming in the Arctic and Subarctic was particularly pronounced. Sampling within a 3‐week time window each summer demonstrated that trends in the overall abundance of C. finmarchicus varied between years, with the highest values in “extreme” years, due to high numbers of nauplii and early copepodite stages in colder years (2001, 2004, 2010), and contrary to that, the fifth copepodite stage (C5) peaking in warm years (2006, 2007, 2009). The most influential environmental variable driving C. finmarchicus life cycle was temperature, which promoted an increased C5 abundance when the temperature was above 6°C, indicating earlier spawning and/or accelerated development, and possibly leading to their development to adults later in the summer and spawning for the second time, given adequate food supply. Based on the presented high interannual and spatial variability, we hypothesize that under a warmer climate, C. finmarchicus may annually produce two generations in the southern part of the WSC, what in turn could lead to food web reorganization of important top predators, such as little auks, and induce northward migrations of fish, especially the Norwegian herring.