Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiological Etiology and Treatment of Complicated Skin and Skin Structure Infections in Diabetic and Nondiabetic Patients in a Population-Based Study

Abstract Background Diabetes is a major risk factor for skin and skin structure infection (SSSI), and the global burden of diabetics with SSSI is enormous. The more complex microbiology of diabetic foot infection (DFI) is well established, but it is not known whether microbiological etiology differs between diabetics and nondiabetics in other disease entities under the umbrella of complicated SSSI (cSSSI). Methods This retrospective, population-based study included patients with cSSSI, and it was conducted in 2 Nordic cities with a low prevalence of antimicrobial resistance. In analyses, patients (N = 460) were separated into 3 groups: diabetics (n = 119), nondiabetics (n = 271), and patients with DFI (n = 70). Results After exclusion of patients with DFI, there was no difference in the microbiological etiology or initial antimicrobial treatment of cSSSI between diabetics and nondiabetics. Gram-positive bacteria encountered 70% of isolations in diabetics and 69% in nondiabetics, and the empirical treatment covered initial pathogens in 81% and 86% of patients, respectively. However, diabetes was the only background characteristic in the propensity score-adjusted analysis associated with broad-spectrum antimicrobial use and longer antibiotic treatment duration. Patients with DFI had Gram-negative and polymicrobial infection more often than nondiabetics. Conclusions These observations suggest that diabetics without DFI are not different in the causative agents of cSSSI, although they are more exposed to antimicrobial therapy of inappropriate extended spectrum and long duration. Broad-spectrum coverage was clearly needed only in DFI. A clear opportunity for antimicrobial stewardship was detected in the rapidly growing population of diabetic patients with cSSSI.
Effect of Manual Editing of Total Recording Time: Implications for Home Sleep Apnea Testing.

STUDY OBJECTIVES Type 3 home sleep apnea tests may underestimate the apnea-hypopnea index (AHI) due to overestimation of total sleep time (TST). We aimed to evaluate the effect of manual editing of the total recording time (TRT) on the TST and AHI. METHODS Thirty 15-channel in-home polysomnography studies (AHI 0 to 30 events/h) scored using American Academy of Sleep Medicine criteria were rescored by two blinded polysomnologists after data from electroencephalogram, electrooculogram, and electromyogram were masked. In method 1, periods of probable wakefulness and artifact were manually edited and removed from analysis. Method 2 identified TST as the TRT without manual editing. Paired t-tests were used to compare the TST and AHI between these methods. Sensitivity and specificity of each method were calculated for gold standard AHI cutoffs of ≥ 5 and ≥ 15 events/h. RESULTS TST (mean [standard deviation, SD]) by polysomnography, method 1, and method 2 was 366.0 (70.1), 447.1 (59.0), and 542 (61.9) min, respectively. The corresponding AHI was 12.5 (8.2), 10.8 (7.0), and 9.1 (6.1) events/h, respectively. Compared to polysomnography, both alternative methods overestimated the TST (method 1: mean difference [SD] 81.1 [56.1] min, method 2: 176.0 [89.7] min; both p < 0.001) and underestimated the AHI (method 1: mean difference [SD] -1.6 [3.3], method 2: -3.3 [3.9]; both p < 0.001). The sensitivity was 100% and 70.0% for method 1, and 91.3% and 40.0% for method 2 for identifying sleep-disordered breathing using AHI cutoffs of ≥ 5 and ≥ 15 events/h, respectively. CONCLUSIONS Manual editing of TRT reduces the overestimation of TST and improves the sensitivity for identifying studies with sleep-disordered breathing. COMMENTARY A commentary on this article appears in this issue on page 9.
Validating a Predictive Model of Acute Advanced Imaging Biomarkers in Ischemic Stroke

Background and Purpose— Advanced imaging to identify tissue pathophysiology may provide more accurate prognostication than the clinical measures used currently in stroke. This study aimed to derive and validate a predictive model for functional outcome based on acute clinical and advanced imaging measures. Methods— A database of prospectively collected sub-4.5 hour patients with ischemic stroke being assessed for thrombolysis from 5 centers who had computed tomographic perfusion and computed tomographic angiography before a treatment decision was assessed. Individual variable cut points were derived from a classification and regression tree analysis. The optimal cut points for each assessment variable were then used in a backward logic regression to predict modified Rankin scale (mRS) score of 0 to 1 and 5 to 6. The variables remaining in the models were then assessed using a receiver operating characteristic curve analysis. Results— Overall, 1519 patients were included in the study, 635 in the derivation cohort and 884 in the validation cohort. The model was highly accurate at predicting mRS score of 0 to 1 in all patients considered for thrombolysis therapy (area under the curve [AUC] 0.91), those who were treated (AUC 0.88) and those with recanalization (AUC 0.89). Next, the model was highly accurate at predicting mRS score of 5 to 6 in all patients considered for thrombolysis therapy (AUC 0.91), those who were treated (0.89) and those with recanalization (AUC 0.91). The odds ratio of thrombolysed patients who met the model criteria achieving mRS score of 0 to 1 was 17.89 (4.59–36.35, P<0.001) and for mRS score of 5 to 6 was 8.23 (2.57–26.97, P<0.001). Conclusions— This study has derived and validated a highly accurate model at predicting patient outcome after ischemic stroke.
Evidence That Adrenergic Ventrolateral Medullary Cells Are Activated whereas Precerebellar Lateral Reticular Nucleus Neurons Are Suppressed during REM Sleep

Rapid eye movement sleep (REMS) is generated in the brainstem by a distributed network of neurochemically distinct neurons. In the pons, the main subtypes are cholinergic and glutamatergic REMS-on cells and aminergic REMS-off cells. Pontine REMS-on cells send axons to the ventrolateral medulla (VLM), but little is known about REMS-related activity of VLM cells. In urethane-anesthetized rats, dorsomedial pontine injections of carbachol trigger REMS-like episodes that include cortical and hippocampal activation and suppression of motoneuronal activity; the episodes last 4–8 min and can be elicited repeatedly. We used this model to determine whether VLM catecholaminergic cells are silenced during REMS, as is typical of most aminergic neurons studied to date, and to investigate other REMS-related cells in this region. In 18 anesthetized, paralyzed and artificially ventilated rats, we obtained extracellular recordings from VLM cells when REMS-like episodes were elicited by pontine carbachol injections (10 mM, 10 nl). One major group were the cells that were activated during the episodes (n = 10). Their baseline firing rate of 3.7±2.1 (SD) Hz increased to 9.7±2.1 Hz. Most were found in the adrenergic C1 region and at sites located less than 50 µm from dopamine β-hydroxylase-positive (DBH+) neurons. Another major group were the silenced or suppressed cells (n = 35). Most were localized in the lateral reticular nucleus (LRN) and distantly from any DBH+ cells. Their baseline firing rates were 6.8±4.4 Hz and 15.8±7.1 Hz, respectively, with the activity of the latter reduced to 7.4±3.8 Hz. We conclude that, in contrast to the pontine noradrenergic cells that are silenced during REMS, medullary adrenergic C1 neurons, many of which drive the sympathetic output, are activated. Our data also show that afferent input transmitted to the cerebellum through the LRN is attenuated during REMS. This may distort the spatial representation of body position during REMS.
Chronic Chlamydia pneumoniae infection and bronchial asthma: is there a link?

PURPOSE Besides well-defined environmental causes, accumulating evidence suggests that respiratory tract infections play an important role in the pathogenesis of asthma. Among these Chlamydia pneumoniae infection has been discussed as possibly inducing the development of asthma. METHODS This study was designed to investigate the presence of anti chlamydial IgG, IgA, and IgM antibodies by ELISA in serum samples of 60 adults with a clinical history of asthma and 100 healthy age and sex matched controls. All the samples positive for Chlamydial genus specific IgG antibodies were then subjected to Chlamydia pneumoniae species specific IgG antibody ELISA. RESULTS The IgG anti chlamydial antibody-positivity rate in the patients with bronchial asthma (80%) was significantly higher in all age groups than that in the healthy age and sex matched controls (59%). No significant association was observed for IgA and IgM anti chlamydial antibodies. C. pneumoniae species specific IgG antibody seroprevalence was also found to be significantly higher in all age groups in comparison to controls (61.66% vs 38%). CONCLUSIONS Serological evidence of chronic infection with C. pneumoniae was more frequent in patients with asthma compared with control subjects. Our results support the correlation of bronchial asthma and chronic infection with C. pneumoniae in Indian population.
MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi. nlm.nih. gov/projects/mutabind/.
Multi-target stool DNA test in the surveillance of inflammatory bowel disease: a cross-sectional cohort study

Abstract Background and aim: Colonoscopic surveillance is recommended in patients with longstanding inflammatory bowel disease (IBD) as they are at increased risk of colorectal cancer (CRC). Non-invasive surveillance may improve compliance and access. Multi-target stool DNA (MT-sDNA) has been validated for screening of sporadic CRC but has not been assessed in IBD. Our aim was to assess the performance of a MT-sDNA test in a real-life surveillance setting of patients with longstanding IBD. Material and methods: A total of 192 IBD patients enrolled from two prospective cohorts submitted an EDTA buffered stool sample and underwent chromo- or white light colonoscopy. Stools were assayed for methylated BMP3 & NDRG4, mutant KRAS and β-actin by a laboratory blinded to clinical data. Results: The multitarget-sDNA panel was positive in 2/2 CRC and 5/15 low-grade dysplasia (LGD) < 1 cm in diameter. Sensitivities were 100% (95% CI 16–100%) for CRC and 33% (95% CI 13–61%) for LGD lesions <1 cm, with specificities of 87% (95% CI 81–91%) and 93% (95% CI 88–96%), respectively. The estimated number of patients needed to screen to detect a single CRC was 96 (95% CI 93–99%) and was 28 (95% CI 22–34%) to detect any colorectal neoplasia (CRN). Conclusion: The MT-sDNA panel detected CRC in IBD. Sensitivity for sub-centimeter colorectal neoplasms in IBD patients appears similar to that observed in the general population. The test may be a valuable tool for detection of malignancy during structured surveillance of long-term IBD in a first line hospital setting.
Hydrolysable tannin-based diet rich in gallotannins has a minimal impact on pig performance but significantly reduces salivary and bulbourethral gland size

Tannins have long been considered ‘anti-nutritional’ factors in monogastric nutrition, shown to reduce feed intake and palatability. However, recent studies revealed that compared with condensed tannins, hydrolysable tannins (HT) appear to have far less impact on growth performance, but may be inhibitory to the total activity of caecal bacteria. This in turn could reduce microbial synthesis of skatole and indole in the hindgut of entire male pigs (EM). Thus, the objective of this study was to determine the impact of a group of dietary HT on growth performance, carcass traits and boar taint compounds of group housed EM. For the study, 36 Swiss Large White boars were assigned within litter to three treatment groups. Boars were offered ad libitum one of three finisher diets supplemented with 0 (C), 15 (T15) or 30 g/kg (T30) of HT from day 105 to 165 of age. Growth performance, carcass characteristics, boar taint compounds in the adipose tissue and cytochrome P450 (CYP) isoenzymes CYP2E1, CYP1A2 and CYP2A19 gene expression in the liver was assessed. Compared with C, feed efficiency but not daily gain and daily feed intake was lower (P<0.05) in T15 and T30 boars. Except for the percentage carcass weight loss during cooling, which tended (P<0.10) to be greater in T30 than C and T15, carcass characteristics were not affected by the diets. In line with the numerically lower androstenone level, bulbourethral and salivary glands of T30 boars were lighter (P<0.05) than of T15 with intermediate values for C. Indole level was lower (P<0.05) in the adipose tissue of T30 than C pigs with intermediate levels in T15. Skatole levels tended (P<0.10) to be lower in T30 and C than T15 pigs. Hepatic gene expression of CYP isoenzymes did not differ between-treatment groups, but was negatively correlated (P<0.05) with androstenone (CYP2E1 and CYP1A2), skatole (CYP2E1, CYP2A) and indole (CYP2A) level. In line with the numerically highest androstenone and skatole concentrations, boar taint odour but not flavour was detected by the panellists in loins from T15 compared with loins from C and T30 boars. These results provide evidence that HT affected metabolism of indolic compounds and androstenone and that they affected the development of accessory sex glands. However, the effects were too small to be detected by sensory evaluation.
Quantification of lung abnormalities in cystic fibrosis using deep networks

Cystic fibrosis is a genetic disease which may appear in early life with structural abnormalities in lung tissues. We propose to detect these abnormalities using a texture classification approach. Our method is a cascade of two convolutional neural networks. The first network detects the presence of abnormal tissues. The second network identifies the type of the structural abnormalities: bronchiectasis, atelectasis or mucus plugging.We also propose a network computing pixel-wise heatmaps of abnormality presence learning only from the patch-wise annotations. Our database consists of CT scans of 194 subjects. We use 154 subjects to train our algorithms and the 40 remaining ones as a test set. We compare our method with random forest and a single neural network approach. The first network reaches a sensitivity of 0,62 for disease detection, 0,10 higher than the random forest classifier and 0,17 higher than the single neural network. Our cascade approach yields a final class-averaged F1-score of 0,38, outperforming the baseline method and the single network by 0,15 and 0,10 .
Prostate cancer: what about reproducibility of decision made at multidisciplinary team management?

PURPOSE The prostate cancer (PCa) treatment is multimodal. Thus multidisciplinary team management (MDTM) decision-making process appears as a tool to answer all aspects of PCa treatment. Our aim was to evaluate the reproducibility of therapeutic decisions made at MDTM. MATERIALS AND METHODS We compared therapeutic decisions of PCa by presenting the same file of patient under a fake identity after 6 to 12 months from the first presentation. Forty-nine files of radical prostatectomy (RP) (28 pT2, 21 pT3) performed for clinical localized PCa were represented at MDTM which included urologist, oncologist, pathologist and radiologist. Analysis of therapeutic decisions comprised criteria such as: TNM stage, Gleason score, margin status and comorbidities. The reproducibility was assessed statistically by Kappa coefficient. RESULTS Study subjects included 49 patients who underwent radical prostatectomy (RP). The mean age was similar in pT2 and pT3 groups (P = .09). The mean serum PSA value was 8.32 ng/mL (range, 3.56-19.5) in pT2 group and 9.4 ng/mL (range, 3.8-22) in pT3 group. The margin status in pT2 and pT3 groups was positive in 25.0% and 47.6%, respectively. The decisions made at first and second MDTM for pT2 group were the same in 100% of cases with a perfect kappa coefficient (k = 1). In the group of pT3 (n = 21), the decisions were different in 33% at the second MDTM in comparison to the first MDTM. Especially for pT3b only 29% were reproducible decision with a slight agreement (k = 0.1). Concerning pT3a, 86% of the decisions were reproducible with a substantial agreement (k = 0.74). CONCLUSION We showed a reliability and reproducibility of decision made at MDTM when guidelines are well defined. The therapeutic attitudes were less reproducible in locally advanced PCa but decision concerning those cases should be made in the setting of guidelines.
Anxiety and depressive symptoms in women and men from early pregnancy to 30 months postpartum

Abstract Aims: The aims of this study were to analyse the changes in anxiety and depression symptoms from early pregnancy to 30 months postpartum according to gender and parity. Method: 129 couples (N = 258) recruited from an obstetrics unit completed self-report measures of anxiety and depression at each pregnancy trimester, childbirth, 3 and 30 months postpartum. Using multilevel modelling, piecewise dyadic growth curve models were performed, assessing time, gender and parity as predictors of anxiety and depression symptoms. Results: Anxiety and depression symptoms decreased from the first trimester to 3 months postpartum and increased from 3 to 30 months postpartum, returning to the baseline levels in the overall sample. The symptoms were positively correlated within-dyad; in a given time point when a partner reported more symptoms, the other reported more symptoms as well. Changes in anxiety and depression symptoms over time were different according to gender and parity, especially from 3 to 30 months postpartum. Primiparous women revealed low stable symptoms, whereas multiparous women revealed the steepest symptoms increase (in comparison to primiparous men and women and multiparous men). Conclusions: This study corroborates the literature considering that the transition to parenthood can last until the child’s age of 2 or 3 years. Results point out that the risk for anxiety and depression symptoms increasing over the postpartum period is greater for multiparous and lesser for primiparous women. Future studies should explore the factors that contribute to the high risk of symptoms increase over the postpartum period for multiparous women. Screening and intervention should target couples and not only women.
Self-determination and expectancy-value: Comparison of cognitive psychological approaches to motivators for information seeking about job opportunities

Purpose This article elaborates the picture of the motivators for information seeking by comparing two cognitive psychological approaches to motivation: self-determination theory (SDT) and expectancy-value theories (EVTs). Design/methodology/approach The study draws on the conceptual analysis of 31 key investigations characterizing the nature of the above theories. Their potential is examined in light of an illustrative example of seeking information about job opportunities. Findings SDT approaches motivation by examining the degree to which one can make volitional choices while meeting the needs of autonomy and competence. Information-seeking behaviour is most volitional when it is driven by intrinsic motivation, while such behaviours driven by extrinsic motivation and amotivation are less volitional. Modern EVTs approach the motivators for information seeking by examining the individual´s beliefs related to intrinsic enjoyment, attainment value, utility value and relative cost of information seeking. Bo.
Vibrational spectra and topological structure of tetrahedrally bonded amorphous semiconductors

Abstract Calculations of the vibrational spectra of continuous random network models of tetrahedrally bonded amorphous semiconductors are presented. Nearest neighbour central and non-central force constants are used. The results show that the shape of the TO-like peak of the spectrum depends on both the topology and bondangle distribution of the network. Comparison with experimental data suggests that a-Ge contains slightly fewer odd-membered rings than the Polk model and an average bond-angle distortion of 10° or more. On the other hand the shape of the TA-like peak depends more directly on the topology of the network, giving a clearer distinction between the results for structures containing both odd and evenmembered rings and those containing even rings only. Tentative comparison with experimental data for a-GaAs suggests a structure containing very few oddmembered rings, while the data for a-Ge indicate a significant number of oddmembered rings.
High-Quality Diets Associate With Reduced Risk of Colorectal Cancer: Analyses of Diet Quality Indexes in the Multiethnic Cohort.

BACKGROUND & AIMS Healthy eating patterns assessed by diet quality indexes (DQIs) have been related to lower risk of colorectal cancer-mostly among whites. We investigated the associations between 4 DQI scores (the Healthy Eating Index 2010 [HEI-2010], the Alternative Healthy Eating Index 2010 [AHEI-2010], the alternate Mediterranean diet score [aMED], and the Dietary Approaches to Stop Hypertension score) and colorectal cancer risk in the Multiethnic Cohort. METHODS We analyzed data from 190,949 African American, Native Hawaiian, Japanese American, Latino, and white individuals, 45 to 75 years old, who entered the Multiethnic Cohort study from 1993 through 1996. During an average 16 years of follow-up, 4770 invasive colorectal cancer cases were identified. RESULTS Scores from all 4 DQIs associated inversely with colorectal cancer risk; higher scores associated with decreasing colorectal cancer risk (all P's for trend ≤ .003). Associations were not significant for AHEI-2010 and aMED scores in women after adjustment for covariates: for the highest vs lowest quintiles, the hazard ratio for the HEI-2010 score in men was 0.69 (95% confidence interval [CI], 0.59-0.80) and in women was 0.82 (95% CI, 0.70-0.96); for the AHEI-2010 score the hazard ratio in men was 0.75 (95% CI, 0.65-0.85) and in women was 0.90 (95% CI, 0.78-1.04); for the aMED score the hazard ratio in men was 0.84 (95% CI, 0.73-0.97) and in women was 0.96 (95% CI, 0.82-1.13); for the Dietary Approaches to Stop Hypertension score the hazard ratio in men was 0.75 (95% CI, 0.66-0.86) and in women was 0.86 (95% CI, 0.75-1.00). Associations were limited to the left colon and rectum for all indexes. The inverse associations were less strong in African American individuals than in the other 4 racial/ethnic groups. CONCLUSIONS Based on an analysis of data from the Multiethnic Cohort Study, high-quality diets are associated with a lower risk of colorectal cancer in most racial/ethnic subgroups.