Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man

SUMMARY Suspensions of isolated epithelial cells (colonocytes) from the human colon were used to assess utilisation of respiratory fuels which are normally available to the colonic mucosa in vivo. Cells were prepared from operative specimens of the ascending colon (seven) and descending colon (seven). The fuels that were used were the short chain fatty acid n-butyrate, produced only by anaerobic bacteria in the colonic lumen, together with glucose and glutamine, normally present in the circulation. The percentage oxygen consumption attributable to n-butyrate, when this was the only substrate, was 7301 in the ascending colon and 750% in the descending colon. In the presence of 10 mM glucose these proportions changed to 59%0 and 72%. Aerobic glycolysis was observed in both the ascending and descending colon. Glucose oxidation accounted for 85% of the oxygen consumption in the ascending colon and 300/ in the descending colon. In the presence of 10 mM n-butyrate these proportions decreased to 41% in the ascending colon and 16% in the descending colon. Based on the assumption that events in the isolated colonocytes reflect utilization of fuels in vivo, the hypothesis is put forward that fatty acids of anaerobic bacteria are a major source of energy for the colonic mucosa, particularly of the distal colon. The mucosa
Epidemiological Characteristics and Survival Studies of Rhabdomyosarcoma in East Egypt: A Five-Year Multicenter Study

Background. Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, it represents 5–8% of childhood malignancies. Aim of the Work. To evaluate the epidemiological characteristics and treatment outcome in two pediatric oncology centers. Patients and Method. A retrospective analysis was performed on 41 medical records of children with RMS during 6 years period. Results. The median age of patients was 6 years with 80.4% below 10 years. Head and neck was the most common primary site. Embryonal RMS was the most frequent histopathologic subtype. Stage IV was the most frequent stage. According to IRS postsurgical grouping classification, group 4 was the most frequent group. There was a significant relationship between histopathologic subtypes of tumor and metastasis, primary site of tumor and histopathologic subtype, age, metastasis, IRS presurgical stage and IRS postsurgical group and outcome. The overall survival rate was 56.9% ± 8.4 and the failure free survival rate was 68.3% ± 7.6. Conclusion. The epidemiological characteristics of our patients are quite near to the worldwide data, apart from the higher prevalence of stage IV and group 4 with most of the primary tumor site in the extremities. CWS2002 protocol of therapy had led to improvement in the curability of the disease.
Practice Parameter update: Evaluation and management of driving risk in dementia

Objective: To review the evidence regarding the usefulness of patient demographic characteristics, driving history, and cognitive testing in predicting driving capability among patients with dementia and to determine the efficacy of driving risk reduction strategies. Methods: Systematic review of the literature using the American Academy of Neurology's evidence-based methods. Recommendations: For patients with dementia, consider the following characteristics useful for identifying patients at increased risk for unsafe driving: the Clinical Dementia Rating scale (Level A), a caregiver's rating of a patient's driving ability as marginal or unsafe (Level B), a history of crashes or traffic citations (Level C), reduced driving mileage or self-reported situational avoidance (Level C), Mini-Mental State Examination scores of 24 or less (Level C), and aggressive or impulsive personality characteristics (Level C). Consider the following characteristics not useful for identifying patients at increased risk for unsafe driving: a patient's self-rating of safe driving ability (Level A) and lack of situational avoidance (Level C). There is insufficient evidence to support or refute the benefit of neuropsychological testing, after controlling for the presence and severity of dementia, or interventional strategies for drivers with dementia (Level U).
Deep Fisher Networks for Large-Scale Image Classification

As massively parallel computations have become broadly available with modern GPUs, deep architectures trained on very large datasets have risen in popularity. Discriminatively trained convolutional neural networks, in particular, were recently shown to yield state-of-the-art performance in challenging image classification benchmarks such as ImageNet. However, elements of these architectures are similar to standard hand-crafted representations used in computer vision. In this paper, we explore the extent of this analogy, proposing a version of the state-of-the-art Fisher vector image encoding that can be stacked in multiple layers. This architecture significantly improves on standard Fisher vectors, and obtains competitive results with deep convolutional networks at a smaller computational learning cost. Our hybrid architecture allows us to assess how the performance of a conventional hand-crafted image classification pipeline changes with increased depth. We also show that convolutional networks and Fisher vector encodings are complementary in the sense that their combination further improves the accuracy.
Assessing a Group of Physicians’ Ethical Sensitivity in Turkey

Background: The objective was to measure the sensitivity of a group of physicians regarding the ethics-related situations, which they faced during patient care and treatment. Methods: All of 306 physicians who joined the Turkish Army for compulsory military service in December 2008 were included in the study. A “Moral Sensitivity Questionnaire”, formed by Kim Lutzen, was applied to all of them. Results: From total, 95% of physicians performed their job willingly, 88% of physicians attended ethic lessons (n=265), 72.4% (n=218) followed ethic publications, 67.4% (n=203) stated that there was an ethic committee at their institutions, and 5% worked as a member of the ethic committee. There were statistically significant differences between autonomy, benevolence meaning, conflict, and total scores according to workplace of physicians, employment period, and being specialists. Points of autonomy were found lower in physicians working at private hospital and health center than those at public hospital. Conclusion: Ethical sensitivity of physicians changed due to work place. We conclude that organizational arrangements are of beneficial effects to increase ethical sensitivity.
Adenosine Deaminase Acting on RNA-1 (ADAR1) Inhibits HIV-1 Replication in Human Alveolar Macrophages

While exploring the effects of aerosol IFN-γ treatment in HIV-1/tuberculosis co-infected patients, we observed A to G mutations in HIV-1 envelope sequences derived from bronchoalveolar lavage (BAL) of aerosol IFN-γ-treated patients and induction of adenosine deaminase acting on RNA 1 (ADAR1) in the BAL cells. IFN-γ induced ADAR1 expression in monocyte-derived macrophages (MDM) but not T cells. ADAR1 siRNA knockdown induced HIV-1 expression in BAL cells of four HIV-1 infected patients on antiretroviral therapy. Similar results were obtained in MDM that were HIV-1 infected in vitro. Over-expression of ADAR1 in transformed macrophages inhibited HIV-1 viral replication but not viral transcription measured by nuclear run-on, suggesting that ADAR1 acts post-transcriptionally. The A to G hyper-mutation pattern observed in ADAR1 over-expressing cells in vitro was similar to that found in the lungs of HIV-1 infected patients treated with aerosol IFN-γ suggesting the model accurately represented alveolar macrophages. Together, these results indicate that ADAR1 restricts HIV-1 replication post-transcriptionally in macrophages harboring HIV-1 provirus. ADAR1 may therefore contribute to viral latency in macrophages.
Urinary incontinence is associated with the development of peptic ulcers in adult women

Abstract The aim of this study was to investigate the association between urinary incontinence (UI) and peptic ulcer (PU) and how this is related to psychological stress in Korean women by analyzing the data from the Korea National Health and Nutrition Examination Survey IV (KNHANES). A nationally representative sample of data on 7475 Korean women ≥19 years of age from the KNHANES 2008 to 2010 was included. Physician-diagnosed UI and PU were assessed using questionnaires and surveys. Psychological stress was assessed through a questionnaire using a 4-point Likert scale. Data were analyzed using logistic regression to determine the association between UI and PU according to the level of psychological stress perception. PU was found in 1.41% of the total population. Breaking this down by the existence of UI, PU was found in 3.5% of the population with UI, and 1.4% of the population without UI, which showed a significant difference. A statistically significant trend for increasing prevalence of UI and PU with increasing psychological stress perception levels was found among the study population. Multivariable logistic regression analyses for PU showed that UI was significantly associated with a higher probability of PU in an adjusted model, which means that members of the population with UI were more likely to have PU than those without UI. A higher level of psychological stress perception was also significantly associated with increased odds of PU in the adjusted model. UI could potentiate the development of PU through increasing levels of psychological stress perception.
Loss of orphan receptor small heterodimer partner sensitizes mice to liver injury from obstructive cholestasis

The orphan nuclear hormone receptor small heterodimer partner (SHP) regulates the expression of several genes involved in bile acid homeostasis in the liver. Because bile acid toxicity is a major source of liver injury in cholestatic disease, we explored the role of SHP in liver damage induced by common bile duct ligation (BDL). Shp−/− mice show increased sensitivity in this model of acute obstructive cholestasis, with greater numbers of bile infarcts and higher mortality than wild‐type C57BL/6 mice. This increased sensitivity could not be accounted for by differences in expression of bile acid homeostatic genes 2 or 5 days after BDL. Instead, higher basal expression of such genes, including the key biosynthetic enzyme cholesterol 7α hydroxylase (Cyp7A1) and the bile salt export pump, is associated with both an increase in bile flow prior to BDL and an increase in acute liver damage at only 1.5 hours after BDL in Shp−/− mice, as shown by bile infarcts. At 3 hours, Cyp7A1 expression still remained elevated in Shp−/− with respect to wild‐type mice, and the hepatic and serum bile acid levels and total hepatobiliary bile acid pool were significantly increased. The increased sensitivity of mice lacking SHP contrasts with the decreased sensitivity of mice lacking the farnesoid X receptor (FXR; nuclear receptor subfamily 1, group H, member 4) to BDL, which has been associated with decreased intraductal pressure and fewer bile infarcts. Conclusion: We propose that differences in acute responses to BDL, particularly the early formation of bile infarcts, are a primary determinant of the differences in longer term sensitivity of the Fxr−/− and Shp−/− mice to acute obstructive cholestasis. (HEPATOLOGY 2008.)
Evaluation of a Decision-support System for Preoperative Staging of Prostate Cancer

The usefulness and effectiveness of a decision-support system for preoperative stag ing of prostate cancers (PCES) were evaluated. The study population consisted of 43 consecutive patients with the preoperative diagnosis of prostate cancer who underwent surgical operation. Results obtained using the PCES were compared with staging by four urology attending physicians and five urology residents. The effect of PCES con sultation on the physicians' staging of prostate cancer was also evaluated. To confirm the usefulness of the clinical findings of prostate-specific antigen, prostate-specific an tigen density, prostate volume, and abnormal Gleason score in the PCES, their re ceiver operating characteristic (ROC) curves for diagnosis of advanced prostate cancer were plotted. The values of the areas under the curves were 0.772, 0.800, 0.531, and 0.752. The stage of prostate cancer was correctly determined by the PCES for 38 of the 43 patients, yielding 88.4% preoperative diagnostic accuracy. The PCES was sig nificantly more accurate than two of the attending physicians and all residents. PCES consultation improved the residents' staging accuracy to approximately that of the at tending physicians. The effect of PCES consultation on the residents' staging was significantly (p < 0.001) greater than the effect on the physicians' staging. The PCES may be useful in the preoperative staging of prostate cancers, especially during resi dency. The system's accuracy in determining the stage of advanced prostate cancer may make it possible to avoid unneccesary surgical operations. Key words: decision- support system; expert system; prostate cancer. (Med Decis Making 1999;19:419- 427)
The Effects of Auditory Contrast Tuning upon Speech Intelligibility

We have previously identified neurons tuned to spectral contrast of wideband sounds in auditory cortex of awake marmoset monkeys. Because additive noise alters the spectral contrast of speech, contrast-tuned neurons, if present in human auditory cortex, may aid in extracting speech from noise. Given that this cortical function may be underdeveloped in individuals with sensorineural hearing loss, incorporating biologically-inspired algorithms into external signal processing devices could provide speech enhancement benefits to cochlear implantees. In this study we first constructed a computational signal processing algorithm to mimic auditory cortex contrast tuning. We then manipulated the shape of contrast channels and evaluated the intelligibility of reconstructed noisy speech using a metric to predict cochlear implant user perception. Candidate speech enhancement strategies were then tested in cochlear implantees with a hearing-in-noise test. Accentuation of intermediate contrast values or all contrast values improved computed intelligibility. Cochlear implant subjects showed significant improvement in noisy speech intelligibility with a contrast shaping procedure.
Accounts of carers' satisfaction with health care at the end of life: A comparison of first generation black Caribbeans and white patients with advanced disease

While much research has described experiences at the end of life, no studies have explored the black Caribbean perspective. This paper compares the final year of life of first generation black Caribbeans and white patients with advanced disease in an inner London health authority, focusing on their satisfaction with service provision in both primary care and acute settings using face-to face interviews with carers of deceased patients. Of the 106 black Caribbean patients and 110 white deceased patients identified as dying during the study period 50 interviews per ethnic group were conducted with family members or close friends, a response rate of 47% and 45%. Even though examples of excellent and good care were cited, a larger proportion of negative satisfaction ratings of health care was recorded among respondents representing black Caribbean patients. This was true for all health care settings, particularly primary care, but less so for specialist palliative care nurses. However, few black Caribbean patients accessed specialist palliative care nurses or hospices. Qualitative data provided a deeper insight into the black Caribbean experience care at the end of life. We recommend that where examples of best practice in palliative care and culturally sensitive provision are evident they be extended to more health care professionals through education and training. Access to specialist palliative care services needs to be improved.
Selective bispecific T cell recruiting antibody and antitumor activity of adoptive T cell transfer.

BACKGROUND One bottleneck for adoptive T cell therapy (ACT) is recruitment of T cells into tumors. We hypothesized that combining tumor-specific T cells, modified with a marker antigen and a bispecific antibody (BiAb) that selectively recognizes transduced T cells and tumor cells would improve T cell recruitment to tumors and enhance therapeutic efficacy. METHODS SV40 T antigen-specific T cells from T cell receptor (TCR)-I-transgenic mice were transduced with a truncated human epidermal growth factor receptor (EGFR) as a marker protein. Targeting and killing by combined ACT and anti-EGFR-anti-EpCAM BiAb therapy was analyzed in C57Bl/6 mice (n = six to 12 per group) carrying subcutaneous tumors of the murine gastric cancer cell line GC8 (SV40(+) and EpCAM(+)). Anti-EGFR x anti-c-Met BiAb was used for targeting of human tumor-specific T cells to c-Met(+) human tumor cell lines. Differences between experimental conditions were analyzed using the Student's t test, and differences in tumor growth with two-way analysis of variance. Overall survival was analyzed by log-rank test. All statistical tests were two-sided. RESULTS The BiAb linked EGFR-transduced T cells to tumor cells and enhanced tumor cell lysis. In vivo, the combination of ACT and Biab produced increased T cell infiltration of tumors, retarded tumor growth, and prolonged survival compared with ACT with a control antibody (median survival 95 vs 75 days, P < .001). In human cells, this strategy enhanced recruitment of human EGFR-transduced T cells to immobilized c-Met and recognition of tyrosinase(+) melanoma cells by TCR-, as well as of CEA(+) colon cancer cells by chimeric antigen receptor (CAR)-modified T cells. CONCLUSIONS BiAb recruitment of tumor-specific T cells transduced with a marker antigen to tumor cells may enhance efficacy of ACT.
Effects of enzymatic treatments on the mechanical properties of corn husk fibers

Corn husk fibers were extracted by water retting, alkalization, and enzymatic processes at different concentration and duration levels. The effects of extraction process parameters on the mechanical and thermal properties and chemical characteristics of corn husk fibers were investigated. Chemical structures of the fibers were studied by IR measurements. The finest and the stiffest fibers were produced by water retting followed by an enzymatic treatment. The highest breaking strength and breaking tenacity were obtained by water-retted fibers. While resulting in loss of breaking tenacity and elongation in water-retted fibers, enzymatic treatment resulted in increase in initial moduli and breaking tenacity of alkalized fibers. No significant effect of enzymatic treatment duration was obtained on the mechanical properties of corn husk fibers. Alkalized fibers gave higher elongation and lower stiffness compared to water-retted ones. The IR spectra showed higher amount of lignin and hemicellulose in water-retted fibers compared to alkalized and enzyme-treated ones. Enzymatic treatment and alkalization enhanced the thermal durability of the fibers. The ranges for properties of the produced corn husk fibers can be summarized as a linear density 17.0–25.6 tex, initial modulus 150.9–401.8 cN/tex, breaking tenacity 6.8–21.7 cN/tex, and elongation 9.6–18.2%.
Diarrhoea prevention in Bolivia through point-of-use water treatment and safe storage: a promising new strategy

A novel water quality intervention that consists of point-of-use water disinfection, safe storage and community education was field tested in Bolivia. A total of 127 households in two periurban communities were randomized into intervention and control groups, surveyed and the intervention was distributed. Monthly water quality testing and weekly diarrhoea surveillance were conducted. Over a 5-month period, intervention households had 44% fewer diarrhoea episodes than control households (P=0·002). Infants <1 year old (P=0·05) and children 5–14 years old (P=0·01) in intervention households had significantly less diarrhoea than control children. Campylobacter was less commonly isolated from intervention than control patients (P=0·02). Stored water in intervention households was less contaminated with Escherichia coli than stored water in control households (P<0·0001). Intervention households exhibited less E. coli contamination of stored water and less diarrhoea than control households. This promising new strategy may have broad applicability for waterborne disease prevention.
Number and Density of AMPA Receptors in Individual Synapses in the Rat Cerebellum as Revealed by SDS-Digested Freeze-Fracture Replica Labeling

The number of AMPA receptor (AMPAR) is the major determinant of synaptic strength at glutamatergic synapses, but little is known about the absolute number and density of AMPARs in individual synapses. Using SDS-digested freeze-fracture replica labeling, which has high detection efficiency comparable with electrophysiological noise analysis for functional AMPAR, we analyzed three kinds of excitatory synapses in the molecular layer of the adult rat cerebellum. In parallel fiber (PF)–Purkinje cell (PC) synapses, we found large variability in the number (38.1 ± 34.4 particles per synapse, mean ± SD; range, 2–178 particles per synapse) and density (437 ± 277 particles/μm2; range, 48–1210 particles/μm2) of immunogold-labeled AMPARs. Two-dimensional view and high sensitivity of this method revealed irregular-shaped small AMPAR clusters within synapses. Climbing fiber (CF)–PC synapses had higher number of AMPAR labeling (68.6 ± 34.5 particles per synapse) than PF–PC and PF–interneuron synapses (36.8 ± 14.4 particles per synapse). Furthermore, AMPAR density at CF–PC and PF–interneuron synapses was approximately five times higher and more uniform than that at PF–PC synapses. These results suggest input- and target-dependent regulation of AMPAR-mediated synaptic strength.
Light field from micro-baseline image pair

We present a novel phase-based approach for reconstructing 4D light field from a micro-baseline stereo pair. Our approach takes advantage of the unique property of complex steerable pyramid filters in micro-baseline stereo. We first introduce a Disparity Assisted Phase based Synthesis (DAPS) strategy that can integrate disparity information into the phase term of a reference image to warp it to its close neighbor views. Based on the DAPS, an “analysis by synthesis” approach is proposed to warp from one of the input binocular images to the other, and iteratively optimize the disparity map to minimize the phase differences between the warped one and the ground truth input. Finally, the densely and regularly spaced, high quality light field images can be reconstructed using the proposed DAPS according to the refined disparity map. Our approach also solves the problems of disparity inconsistency and ringing artifact in available phase-based view synthesis methods. Experimental results demonstrate that our approach substantially improves both the quality of disparity map and light field, compared with the state-of-the-art stereo matching and image based rendering approaches.
From Structure to Function

There are many levels of protein function, ranging from atomic reorganizations to changes in the development of an organism, but all of them involve binding to other molecules, large and small. Sometimes this specific molecular recognition is the sole biochemical function of a protein, but in other cases the protein also promotes a chemical transformation in the molecule that it binds. This chapter looks first at how the structural features described in Chapter 1 dictate the ability of proteins to recognize specifically and bind a wide variety of ligands. The second part of the chapter looks at how these structural features dictate the ability of proteins to catalyze the wide variety of chemical transformations on which life depends. 2