Miracle-dz/UniFAR-FTUs huggingface dataset:
Utilization of Laparoscopic Colectomy in the United States Before and After the Clinical Outcomes of Surgical Therapy Study Group Trial

Objective: To evaluate the utilization of laparoscopic colectomy (LC) in the United States before and after prospective data supported its use for the treatment of colon cancer. Methods: The Nationwide Inpatient Sample 2001–2003 [before Clinical Outcomes of Surgical Therapy (COST)] and 2005–2007 (after COST) was queried for elective colectomies for both benign and malignant disease. The COST trial was published in 2004; therefore, 2004 data were excluded. Univariate analyses including patient-specific, hospital-specific, and outcome variables were performed. Multivariate logistic regression models and subset analyses were used to evaluate these variables and operative approach by time frame. Results: The query yielded 741,817 elective colectomies (684,969 open and 56,848 laparoscopic). The percentage of elective colectomies performed laparoscopically has increased over time. Laparoscopic colectomy for benign disease increased from 6.2% in 2001–2003 to 11.8% in 2005–2007, while those for colon cancer have increased by a larger percentage, 2.3% to 8.9%. In a multivariate model of patients with colon cancer, the odds ratio (OR) for having a laparoscopic approach after COST was 4.55 (confidence interval 3.81–5.44) compared with before COST. In contrast, for benign disease, the OR was 2.10 (confidence interval 1.79–2.46). Factors predictive of having a laparoscopic approach for cancer have changed very little over time: Patients are more likely to be male, insured, live in areas with the highest incomes, and undergo resection at urban teaching hospitals. Conclusions: Within 3 years after publication of the COST trial, the use of laparoscopic resection for colon cancer approached that of benign disease. However, almost 90% of cases are still performed open and utilization remains influenced by socioeconomic factors.
Genetic Analysis of Helicobacter pylori Strain Populations Colonizing the Stomach at Different Times Postinfection

ABSTRACT Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.
Identification of Ciprofloxacin-ResistantCampylobacter jejuni by Use of a Fluorogenic PCR Assay

ABSTRACT Fluoroquinolones are one class of antimicrobial agents commonly used to treat severe Campylobacter jejuni infection.C. jejuni strains resistant to high levels of the fluoroquinolone ciprofloxacin (MIC ≥16 μg/ml) have been predominantly characterized with a C→T transition in codon 86 ofgyrA. The gyrA gene encodes one subunit of DNA gyrase, which is a primary target for fluoroquinolone antibiotics. This study establishes a rapid PCR-based TaqMan method for identifying ciprofloxacin-resistant C. jejuni strains that carry the C→T transition in codon 86 of gyrA. The assay uses real-time detection, eliminating the need for gel electrophoresis. Optimization of the assay parameters using purified Campylobacter DNA resulted in the ability to detect femtogram levels of DNA. The method should be useful for monitoring the development of ciprofloxacin resistance in C. jejuni. Compiled nucleotide sequence data on the quinolone resistance-determining region of gyrA inCampylobacter indicate that sequence comparison of this region is a useful method for tentative identification ofCampylobacter isolates at the species level.
“Deep” Learning : Detecting Metaphoricity in Adjective-Noun Pairs

Metaphor is one of the most studied and widespread figures of speech and an essential element of individual style. In this paper we look at metaphor identification in Adjective-Noun pairs. We show that using a single neural network combined with pre-trained vector embeddings can outperform the state of the art in terms of accuracy. In specific, the approach presented in this paper is based on two ideas: a) transfer learning via using pre-trained vectors representing adjective noun pairs, and b) a neural network as a model of composition that predicts a metaphoricity score as output. We present several different architectures for our system and evaluate their performances. Variations on dataset size and on the kinds of embeddings are also investigated. We show considerable improvement over the previous approaches both in terms of accuracy and w.r. t the size of annotated training data.
Sea Urchin Bioassays inToxicity Testing: II. SedimentEvaluation

Sea Urchin Bioassays in Toxicity Testing: II. Sediment Evaluation Bioassays on sea urchin early life stages have been used extensively in evaluating the pollution impact on seawater, coastal sediments, and other matrices as soil, freshwater sediment, and industry effluents. Here we review the literature in this field to determine whether testing whole sediment vs. pore water or elutriates by sea urchin bioassays provides a better estimation of actual risk. The present review of our results and from independent groups suggests that testing whole sediment as opposed to other substrates is better suitable, especially when a topographic evaluation of sediment toxicity is required, such as in enclosed bays or in lagoons. Unrestricted to marine sediment, the available methods in testing whole sediment provide an opportunity to test inland, freshwater or terrestrial materials, useful when answering complex mixture questions common to various monitoring and research programs, or for environmental assessment evaluations, or for remediation/ mitigation planning exercises.
Comparing living donor and deceased donor liver transplantation: A matched national analysis from 2007 to 2012

A complete evaluation of living donor liver transplantation (LDLT) in the United States has been difficult because of the persistent low volume and the lack of adequate comparisons with deceased donor liver transplantation (DDLT). Recent reports have suggested outcomes equivalent to those for DDLT, but these studies did not adjust for differences in recipient selection. From a linkage between the University HealthSystem Consortium and Scientific Registry of Transplant Recipients databases, we identified 14,282 patients at 62 centers who underwent DDLT from 2007 to 2012 and 715 patients at 35 centers who underwent LDLT during the same period. Then, we performed 1:1 propensity score matching for 708 LDLT recipients based on age, Model for End‐Stage Liver Disease (MELD) score, and pretransplant patient status. The median follow‐up was 2 years. Compared with DDLT recipients, LDLT recipients were more likely to be white (84.5% versus 72.2%) and female (41.1% versus 31.7%), to have lower MELD scores (15 versus 19), and to be classified preoperatively as independent (65.3% versus 46.7%) and not hospitalized (91.3% versus 78.4%). The posttransplant length of stay (LOS), in‐hospital mortality, costs, and survival were similar between the groups, but LDLT recipients were more likely to be readmitted within 30 days (44.9% versus 37.1%, P = 0.001). After matching, the difference in 30‐day readmission rates persisted (45.1% versus 33.8%, P = 0.001), but there were no differences in the LOS, costs, patient survival, or graft survival. This national report shows that LDLT is associated with higher readmission rates in comparison with DDLT, but the results are comparable for other key patient metrics. Liver Transpl 20:1347‐1355, 2014. © 2014 AASLD.
Prenatal Cocaine Exposure and Infants' Preference for Novelty and Distractibility

The authors used the Fagan Test of Infant Intelligence (J. F. Fagan, L. T. Singer, J. E. Montie, & P. A. Shepherd, 1986) to examine preferences for novelty and to evaluate several indicators of attention (off- and on-task indexes and durations) in 6- and 9-month-old infants who had been prenatally exposed to cigarette smoke only or to cocaine plus other substances. The infants were matched for socioeconomic status. The authors found no group differences in preference for novelty, but the off-task distractibility index and duration were affected by exposure history and showed effects of dosage at the 9-month test time. Infants exposed to cocaine had a higher off-task index and a shorter average off-task look duration than did infants in the other groups. The authors interpreted this pattern of behavior as an indicator of distractibility or stimulation seeking. There were no group differences in measures involving on-task looks or duration at either test time. Correlations between the off-task look index and duration and teratogen use produced moderate correlations at 9 months of age. The authors calculated partial correlations between teratogen exposure and the off-task index at each trimester. Cocaine use during the 1st and 2nd trimesters was significantly correlated with the off-task index at 9 months of age, even when the authors controlled for neonatal measures (e.g., gestational age, birth weight) and during the 1st trimester when they controlled for alcohol and cigarette exposure.
Localized measurement of emergent image frequencies by Gabor wavelets

The authors derive, implement, and demonstrate a computational approach for the measurement of emergent image frequencies. Measuring emergent signal frequencies requires spectral measurements accurate in both frequency and time or space, conflicting requirements that are shown to be balanced by a generalized uncertainty relationship. Such spectral measurements can be obtained from the responses of multiple wavelet-like channel filters that sample the signal spectrum, and that yield a locus of possible solutions for each locally emergent frequency. It is shown analytically that this locus of solutions is maximally localized in both space and frequency if the channel filters used are Gabor wavelets. A constrained solution is obtained by imposing a stabilizing term that develops naturally from the assumptions on the signal. The measurement of frequencies is then cast as an ill-posed extremum problem regularized by the stabilizing term, leading to an iterative constraint propagation algorithm. The technique is demonstrated by application to a variety of 2-D textured images. >
DNA-Rag Protein Interactions in the Control of Selective D Gene Utilization in the TCRβ Locus1

Ordered assembly of Ag receptor genes by VDJ recombination is a key determinant of successful lymphocyte differentiation and function. Control of gene rearrangement has been traditionally viewed as a result of complex reorganization of the nucleochromatin mediated by several nuclear factors. Selective recombination of the variable (V) genes to the diversity (D), but not joining (J), gene segments within the TCRβ locus has been shown to be controlled by recombination signal (RS) sequences that flank the gene segments. Through ex vivo and in vitro recombination assays, we demonstrate that the Rag proteins can discriminate between the RS of the D and J genes and enforce selective D gene incorporation into the TCRβ variable domain in the absence of other nuclear factors or chromatin structure. DNA binding studies indicate that discrimination is not simply caused by higher affinity binding of the Rag proteins to the isolated 12RS of the D as opposed to the J genes. Furthermore, we also demonstrate that the 12RS within the TCRβ locus is functionally inferior to the consensus 12RS. We propose that selective gene segment usage is controlled at the level of differential assembly and/or stability of synaptic RS complexes, and that evolutionary “deterioration” of the RS motifs may have been important to allow the VDJ recombinase to exert autonomous control over gene segment use during gene rearrangement.
CHORDA TENDINEA TENSION.

Tension along chordae tendineae (CTT) was measured in absolute terms in situ and recorded throughout cardiac cycles. The transducers were installed without damage to the LV myocardium or its blood supply. CTT contours paralleled LV pressure traces only during isovolumic pressure development; CTT and LVP were sharply distinct or divergent during other periods of the cardiac cycle. The shape or magnitude of CTT could not be predicted from LVP traces. Hemodynamic and other factors influencing the various phases of CTT contours were investigated. Stroke volume, elastic storage capacity of the arterial tree, presence of a pericardial restraint, and coronary artery pressure influenced the magnitude and shape of CTT traces. Two types of heart failure were differentiated by specific CTT contours.
EFFECTS OF RICE PANICLE AGE ON QUANTITATIVE AND QUALITATIVE INJURY BY THE RICE STINK BUG (HEMIPTERA: PENTATOMIDAE)

Abstract Greenhouse experiments were conducted to evaluate the effects of panicle age on quantitative and qualitative injury caused by rice stink bug, Oebalus pugnax pugnax (Fab.), infestations on rice, Oryza sativa L. The effects were measured at two infestation levels (one and two bugs per panicle) and compared with an undamaged control. Percentage of empty grains and average weight of filled grains (quantitative injury) and percentage of pecky rice (qualitative injury) were evaluated at grain maturity. Regardless of infestation level, insect feeding during anthesis and the early milk stage of grain development (first 8 d after anthesis) caused substantially higher numbers of empty grains than feeding during later grain development and the control. Average grain weights were lower in infestations during anthesis and milk stage and higher in infestations during later grain development and the control. Pecky rice was significantly higher during late milk and soft dough stages, 9-16 d after anthesis, compared with remaining stages of grain development and the control. Injury was greater in the experiment in which panicles were infested with two bugs. Pecky rice was associated with highly significant reductions in germination of the grains. The data suggest that rice is most vulnerable to rice stink bug injury during the first two weeks after anthesis, and that the major effects of stink bug feeding change as panicles age.
Expression of enhancers is altered in Drosophila melanogaster hybrids

SUMMARY The molecular foundations of evolution are difficult to trace because most protein sequences are virtually identical in closely related species. The largest fraction of sequence within the genome, however, is composed of noncoding sequences where regulatory elements locate to various sites. It has been suggested that changes in the activity of these elements may trigger evolutionary change. In Drosophila, the enhancer trap procedure identifies regulatory sequences in the genome after the insertion of a P‐element–based construct. We generated new insertions and characterized their expression domains in the adult eye and larval imaginal disks using the white and LacZ reporter genes. Lines with robust expression patterns in D. melanogaster were analyzed in hybrids to test the conservation of regulatory mechanisms between species. Most of the enhancers used in this study modified their expression in hybrids with the mating species D. mauritiana and D. simulans. Expression changes resulted either in gain or loss of expression and were cell‐type or hybrid‐genome specific. Further characterization of a limited number of enhancers in D. melanogaster showed that expression domains could adapt to changes in cell number during development but not after the completion of cell proliferation. Also, expression of some enhancers appeared to be sensitive to heterochromatin from the Y but not the X chromosome. Taken together, these results demonstrate the high sensitivity of regulatory mechanisms of gene expression as a prime source of evolutionary change and suggest quantitative changes in available transcription factors as one of the mechanisms involved.
Cane dieback of Dawn Seedless table grapevines (Vitis vinifera) in Western Australia caused by Botryosphaeria rhodina

Cane dieback of Dawn Seedless table grapevines in the Carnarvon horticultural district of Western Australia was identified as being caused by the fungal pathogen Botryosphaeria rhodina. Symptoms of cane dieback included progressive death of shoots, canes and trunks. Shoot and cane infections were usually associated with external lesions that were bleached in appearance. Lesions often contained minute black pycnidia (0.1–0.2 mm in diameter) which were initially immersed and later became erumpent. Some shoot and cane lesions were less defined. Mature conidia were ovate (20–25 iim by 15–20 Jim), dark brown and uni-septate with longitudinal striations. Immature conidia were of similar shape and size but were hyaline, and single-celled with no striations. This is the first report of B. rhodina causing significant decline of table grapes in Western Australia.
Clinical staging in bipolar disorder: focus on cognition and functioning.

OBJECTIVE Clinical staging has increasingly been considered suitable for psychiatric disorders such as bipolar disorder. A staging model of bipolar disorder could help clinicians understand the mechanisms underlying the course of the illness and guide prognosis and therapy. This study aimed to investigate differences in functional status and cognitive functioning in patients in different clinical stages of bipolar disorder. METHOD Subjects who met DSM-IV criteria for bipolar disorder (n = 54) were recruited from the Bipolar Disorders Program at Hospital de Clínicas de Porto Alegre (Brazil) from October 2012 to October 2013. All patients had been in remission (score < 7 on the 17-item HDRS and the YMRS) for at least 1 month before assessment. They were classified into 4 clinical stages according to the model described by Kapczinski et al and compared to 43 healthy controls. Functional status was assessed by using the Functioning Assessment Short Test (FAST). Neuropsychological measures were performed to investigate cognitive functioning. RESULTS Significant differences in functional status were found between patients in all stages compared to controls (F = 33.014, P < .001), except for stage I (P = .104). Additionally, a very strong linear association was found between FAST scores and clinical stages, with FAST scores increasing from stage I to IV (F = 149.55, P < .001). In the bipolar group, stage I was associated with better occupational functioning than stage II (F = 48.344, P = .003). Stage IV patients experienced greater impairment in autonomy than stage III patients (F = 26.646, P = .004), and stage III patients experienced poorer autonomy than those in stage II (P = .004). With regard to cognitive measures, patients in late stages (stages III and IV) were more impaired than healthy controls (P < .001). A similar performance was found between patients in early stages (stages I and II) and healthy controls. DISCUSSION This study showed progressive functional changes from stage I to stage IV of bipolar disorder, with a greater impairment in patients in later stages of the illness. FAST scores seem to have a good discriminant ability to distinguish between patients in early versus late stages of bipolar disorder and could therefore contribute to the development of a bipolar disorder staging system.
A Study into Digital Dermatitis Transmission and Bacterial Associated Pathological Changes Involved in the Disease

Digital dermatitis is a highly prevalent painful lesion affecting the feet in dairy cattle. Even though the pathogenesis has been subject of investigation since 1974, there is still a lack of knowledge about the spread of the disease among cows within a herd as well as between herds. The purpose of this study was to monitor transmission of digital dermatitis under experimental conditions between naive heifers and affected animals, to monitor the changes in clinical appearance, microbial colonisation of the skin as lesions progressed and to apply a q-PCR for the detection of Treponema spp. in faecal samples. Eight heifers with clinical normal digital skin were housed with 5 heifers with severe digital dermatitis lesion for 8 weeks on a solid concrete floor with an accumulating layer of slurry. Digital skin was examined daily and lesions were clinically scored. Skin biopsies were taken from the healthy heifers at introduction and weekly from all lesions for histopathological evaluation and fluorescence in situ hybridization. None of the healthy heifers developed digital dermatitis and in 4 out of 5 infected heifers the lesions healed during the study. All samples from healthy skin were negative for Treponema spp. and one sample were positive for Dichelobacter nodosus. Colonization of healthy skin could not be identified in this study. There was no significant relation between clinical scoring of the lesions and histopathological score and the presence of Treponema spp. There were however a significant relation between the prevalence of Treponema spp. in the skin and severity of changes in epidermis and dermis. By qPCR all the healthy heifers were found to excrete Treponema spp. in their faeces.
Studies of tocopherol deficiency in infants and children. IV. The effect of alpha tocopherol on creatinuria in patients with cystic fibrosis of the pancreas and biliary atresia.

A bulb ergographic method for estimating muscle strength was modified to permit quantitative measurements. Studies in a group of 13 convalescent children without muscle disease established the reliability of the method for repeated observations. Forty-five patients with cystic fibrosis, whose clinical conditions appeared stable, were accepted in a double-blind study comparing the effect of tocopherol or a placebo on serum tocopherol, S-GOT, weight gain, subjective improvement, and muscle strength as measured by the ergograph. Measurements were made at the beginning of the study, and 2 and 6 months after beginning tocopheryl acetate (10 mg/kg/day) or placebo therapy. Although statistically significant increases in serum tocopherol, weight, muscle strength, and clinical improvement were found at 2 and 6 months after beginning of the study, there were no significant differences between the two groups, except in serum content of tocopherol. In the tocopherol treated group, serum tocopherol became normal (0.83 to 1.05 mg/100 ml), but remained low (0.20 to 0.33 mg/100 ml) in the placebo group. Although the present study did not demonstrate a clinical functional effect of tocopherol therapy in patients with cystic fibrosis, its administration is recommended because of previously reported biochemical and pathologic evidence of vitamin E deficiency in these subjects.