Miracle-dz/UniFAR-FTUs huggingface dataset:
Postpartum urinary tract infection by mode of delivery: a Danish nationwide cohort study

Objectives To examine the association between postpartum urinary tract infection and intended mode of delivery as well as actual mode of delivery. Design Retrospective cohort study. Setting and participants All live births in Denmark between 2004 and 2010 (n=450 856). Births were classified by intended caesarean delivery (n=45 053) or intended vaginal delivery (n=405 803), and by actual mode of delivery: spontaneous vaginal delivery, operative vaginal delivery, emergency or planned caesarean delivery in labour or prelabour. Primary and secondary outcome measures The primary outcome measure was postpartum urinary tract infection (n=16 295) within 30 days post partum, defined as either a diagnosis of urinary tract infection in the National Patient Registry or redemption of urinary tract infection-specific antibiotics recorded in the Register of Medicinal Product Statistics. Results We found that 4.6% of women with intended caesarean delivery and 3.5% of women with intended vaginal delivery were treated for postpartum urinary tract infection. Women with intended caesarean delivery had a significantly increased risk of postpartum urinary tract infection compared with women with intended vaginal delivery (OR 1.33, 95% CI 1.27 to 1.40), after adjustment for age at delivery, smoking, body mass index, educational level, gestational diabetes mellitus, infection during pregnancy, birth weight, preterm delivery, preterm prelabour rupture of membranes, pre-eclampsia, parity and previous caesarean delivery (adjusted OR 1.24, 95% CI 1.17 to 1.46). Using actual mode of delivery as exposure, all types of operative delivery had an equally increased risk of postpartum urinary tract infection compared with spontaneous vaginal delivery. Conclusions Compared with intended vaginal delivery, intended caesarean delivery was significantly associated with a higher risk of postpartum urinary tract infection. Future studies should focus on reducing routine catheterisation prior to operative vaginal delivery as well as improving procedures related to catheterisation.
Multi-channel Encoder for Neural Machine Translation

Attention-based Encoder-Decoder has the effective architecture for neural machine translation (NMT), which typically relies on recurrent neural networks (RNN) to build the blocks that will be lately called by attentive reader during the decoding process. This design of encoder yields relatively uniform composition on source sentence, despite the gating mechanism employed in encoding RNN. On the other hand, we often hope the decoder to take pieces of source sentence at varying levels suiting its own linguistic structure: for example, we may want to take the entity name in its raw form while taking an idiom as a perfectly composed unit. Motivated by this demand, we propose Multi-channel Encoder (MCE), which enhances encoding components with different levels of composition. More specifically, in addition to the hidden state of encoding RNN, MCE takes 1) the original word embedding for raw encoding with no composition, and 2) a particular design of external memory in Neural Turing Machine NTM) for more complex composition, while all three encoding strategies are properly blended during decoding. Empirical study on Chinese-English translation shows that our model can improve by 6.52 BLEU points upon a strong open source NMT system: DL4MT1. On the WMT14 English-French task, our single shallow system achieves BLEU=38.8, comparable with the state-of-the-art deep models.
Hand pressures during arboreal locomotion in captive bonobos (Pan paniscus)

ABSTRACT Evolution of the human hand has undergone a transition from use during locomotion to use primarily for manipulation. Previous comparative morphological and biomechanical studies have focused on potential changes in manipulative abilities during human hand evolution, but few have focused on functional signals for arboreal locomotion. Here, we provide this comparative context though the first analysis of hand loading in captive bonobos during arboreal locomotion. We quantify pressure experienced by the fingers, palm and thumb in bonobos during vertical locomotion, suspension and arboreal knuckle-walking. The results show that pressure experienced by the fingers is significantly higher during knuckle-walking compared with similar pressures experienced by the fingers and palm during suspensory and vertical locomotion. Peak pressure is most often experienced at or around the third digit in all locomotor modes. Pressure quantified for the thumb is either very low or absent, despite the thumb making contact with the substrate during all suspensory and vertical locomotor trials. Unlike chimpanzees, bonobos do not show a rolling pattern of digit contact with the substrate during arboreal knuckle-walking – instead, we found that digits 3 and 4 typically touch down first and digit 5 almost always made contact with the substrate. These results have implications for interpreting extant and fossilized hand morphology; we expect bonobo (and chimpanzee) bony morphology to primarily reflect the biomechanical loading of knuckle-walking, while functional signals for arboreal locomotion in fossil hominins are most likely to appear in the fingers, particularly digit 3, and least likely to appear in the morphology of the thumb. Highlighted Article: Bonobo digit pressures are significantly greater during arboreal knuckle-walking than during either vertical or suspensory locomotion, and the thumb experiences low or no pressure during all locomotor modes.
Feasibility of Intensity-Modulated and Image-Guided Radiotherapy for Functional Organ Preservation in Locally Advanced Laryngeal Cancer

Purpose The study aims to assess the feasibility of intensity-modulated and image-guided radiotherapy (IMRT, and IGRT, respectively) for functional preservation in locally advanced laryngeal cancer. A retrospective review of 27 patients undergoing concurrent chemoradiation for locally advanced laryngeal cancers (8 IMRT, 19 IGRT) was undertaken. In addition to regular clinical examinations, all patients had PET imaging at 4 months and 10 months after radiotherapy, then yearly. Loco-regional control, speech quality and feeding-tube dependency were assessed during follow-up visits. Results At a median follow-up of 20 months (range 6–57 months), four out of 27 patients (14.8%) developed local recurrence and underwent salvage total laryngectomy. One patient developed distant metastases following salvage surgery. Among the 23 patients who conserved their larynx with no sign of recurrence at last follow-up, 22 (95%) reported normal or near normal voice quality, allowing them to communicate adequately. Four patients (14.8%) had long-term tube feeding-dependency because of severe dysphagia (2 patients) and chronic aspiration (2 patients, with ensuing death from aspiration pneumonia in one patient). Conclusions and Clinical Relevance Functional laryngeal preservation is feasible with IMRT and IGRT for locally advanced laryngeal cancer. However, dysphagia and aspiration remain serious complications, due most likely to high radiation dose delivery to the pharyngeal musculatures.
We Underutilize the Leg Graft

Once hemodialysis patients have exhausted all option for a permanent vascular access in both upper extremities, they are often relegated at many dialysis centers to permanent catheter dependence with all its attendant complications, including infections, frequent dysfunction, and central vein stenosis. This commentary makes the case that thigh grafts are a far superior alternative to dialysis catheters in many of these patients. Technical graft failure may occur in some patients due to severe femoral artery calcification, but screening for calcification by ultrasound or computerized tomography can reduce the likelihood of a technical failure. Placement of a thigh graft may lead to critical lower extremity ischemia, but preoperative screening for peripheral vascular disease should minimize this possibility. Thigh grafts have comparable secondary patency to that obtained with upper extremity grafts. Finally, although the risk of infection is somewhat higher for thigh grafts than upper extremity grafts, it is still much lower than the risk of catheter‐related bacteremia. In summary, thigh grafts should be used much more frequently in patients without an option for an upper extremity access.
The Set of Structural DNA–Nuclear Matrix Interactions in Neurons Is Cell‐Type Specific and Rather Independent of Functional Constraints

In metazoans, nuclear DNA is organized during the interphase in negatively supercoiled loops anchored to a compartment or substructure known as the nuclear matrix. The interactions between DNA and the nuclear matrix (NM) are of higher affinity than those between DNA and chromatin proteins since the last ones do not resist the procedures for extracting the NM. The structural interactions DNA–NM constitute a set of topological relationships that define a nuclear higher order structure (NHOS) although there are further higher order levels of organization within the nucleus. So far, the evidence derived from studies with primary hepatocytes and naïve B lymphocytes indicates that the NHOS is cell‐type specific at the local and at the large‐scale level, and so it has been suggested that such NHOS is primary determined by structural and thermodynamic constraints. We carried out a comparative characterization of the NHOS of postmitotic cortical neurons with that of hepatocytes and naïve B lymphocytes. Our results indicate that the NHOS of neurons is completely different at the large scale and at the local level from that one observed in hepatocytes or in naïve B lymphocytes, confirming on the one hand that the set of structural DNA–NM interactions is cell‐type specific and supporting, on the other hand the notion that structural constraints that impinge on chromosomal DNA and the NM are more important for determining this NHOS than functional constraints related to replication and/or transcription. J. Cell. Biochem. 118: 2151–2160, 2017. © 2016 Wiley Periodicals, Inc.
Is it time for individualized testing in the electroencephalogram (EEG) laboratory?

The interictal electroencephalogram (EEG) has an important role in the classification and treatment of epilepsy. In busy EEG laboratories, valuable resources are used in order to comply with current recommendations regarding the length of EEG recordings. Our aim was to examine the time to first interictal epileptiform discharge (IED) in standard and sleep‐deprived EEGs.
International Journal of Biological & Medical Research Quantification of Tannins, Antioxidant Capacity and Antibacterial Activities of Stem Extracts of Avicennia Marina (l)

Original Article Majority of regular synthetic antibiotics are in the process of being labeled outdated owing to multi drug resistance among pathogens. Consequently researchers are devoting interest towards identification and isolation of potent antibacterial compounds from available herbal sources. Aim: The present study was aimed at evaluation of tannin levels, antioxidant potential and antibacterial activity of Avicennia marina L (AM) extracts on selected Gram positive and Gram negative bacterial species. Methods: Stem extracts prepared in different solvents in the order of increasing polarity (ethyl acetate, acetone, ethanol and methanol) were subjected to – quantification of tannins by Folin-Denis method, antioxidant capacity by ABTS and Blue Cro5 method and antibacterial activity by agar well diffusion method against selected bacterial species. The zones of inhibition obtained were measured and the results were statistically analysed. Results: Tannin level was found to be significantly high in methanol extract followed by that in ethanol, acetone and ethyl acetate. Extract in all the solvents showed antioxidant activity. However, extracts in methanol and ethanol exerted higher potentials. Like wise, extracts in all the solvents showed various degrees of antibacterial activity against the test cultures used. The methanol extract on Bacillus subtilis, Staphylococcus aureus and Streptococcus pyogens exhibited higher activity than that of Gentamicin. Conclusions: The present experimental data reveals that the stem of AM is rich in tannins and exhibits potential antioxidant and antibacterial activities. A comparative analysis is also provided with respect to the solvent used for the study of bioactivities.
Impact of Meat Consumption, Preparation, and Mutagens on Aggressive Prostate Cancer

Background The association between meat consumption and prostate cancer remains unclear, perhaps reflecting heterogeneity in the types of tumors studied and the method of meat preparation—which can impact the production of carcinogens. Methods We address both issues in this case-control study focused on aggressive prostate cancer (470 cases and 512 controls), where men reported not only their meat intake but also their meat preparation and doneness level on a semi-quantitative food-frequency questionnaire. Associations between overall and grilled meat consumption, doneness level, ensuing carcinogens and aggressive prostate cancer were assessed using multivariate logistic regression. Results Higher consumption of any ground beef or processed meats were positively associated with aggressive prostate cancer, with ground beef showing the strongest association (OR = 2.30, 95% CI:1.39–3.81; P-trend = 0.002). This association primarily reflected intake of grilled or barbequed meat, with more well-done meat conferring a higher risk of aggressive prostate cancer. Comparing high and low consumptions of well/very well cooked ground beef to no consumption gave OR's of 2.04 (95% CI:1.41–2.96) and 1.51 (95% CI:1.06–2.14), respectively. In contrast, consumption of rare/medium cooked ground beef was not associated with aggressive prostate cancer. Looking at meat mutagens produced by cooking at high temperatures, we detected an increased risk with 2-amino-3,8-Dimethylimidazo-[4,5-f]Quinolaxine (MelQx) and 2-amino-3,4,8-trimethylimidazo(4,5-f)qunioxaline (DiMelQx), when comparing the highest to lowest quartiles of intake: OR = 1.69 (95% CI:1.08–2.64;P-trend = 0.02) and OR = 1.53 (95% CI:1.00–2.35; P-trend = 0.005), respectively. Discussion Higher intake of well-done grilled or barbequed red meat and ensuing carcinogens could increase the risk of aggressive prostate cancer.
AGO6 Functions in RNA-Mediated Transcriptional Gene Silencing in Shoot and Root Meristems in Arabidopsis thaliana

RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points.
Calcium threshold shift enables frequency-independent control of plasticity by an instructive signal

Significance Instructive signals play an important role in synaptic plasticity and learning. For example, at cerebellar parallel fiber (PF)-Purkinje cell synapses, climbing fiber (CF) coactivation provides an instructive signal that promotes long-term depression (LTD) by amplifying spine calcium transients above a threshold level that, at these synapses, is higher than for LTP induction. Here, we show that the CF instructive signal maintains its control over PF plasticity regardless of the PF synaptic activation frequency, which, on its own, alters spine calcium signaling. We demonstrate that high-frequency stimulation reduces the calcium sensitivity of LTD, resulting from inhibitory calcium/calmodulin-dependent kinase II autophosphorylation at Thr305/306. We propose that this regulatory mechanism causes a horizontal shift of the long-term potentiation/LTD cross-over point, making plasticity independent from absolute calcium amplitudes. At glutamatergic synapses, both long-term potentiation (LTP) and long-term depression (LTD) can be induced at the same synaptic activation frequency. Instructive signals determine whether LTP or LTD is induced, by modulating local calcium transients. Synapses maintain the ability to potentiate or depress over a wide frequency range, but it remains unknown how calcium-controlled plasticity operates when frequency variations alone cause differences in calcium amplitudes. We addressed this problem at cerebellar parallel fiber-Purkinje cell synapses, which can undergo LTD or LTP in response to 1-Hz and 100-Hz stimulation. We observed that high-frequency activation elicits larger spine calcium transients than low-frequency stimulation under all stimulus conditions, but, regardless of activation frequency, climbing fiber (CF) coactivation provides an instructive signal that further enhances calcium transients and promotes LTD. At both frequencies, buffering calcium prevents LTD induction and LTP results instead, identifying the enhanced calcium signal amplitude as the critical parameter contributed by the instructive CF signal. These observations show that it is not absolute calcium amplitudes that determine whether LTD or LTP is evoked but, instead, the LTD threshold slides, thus preserving the requirement for relatively larger calcium transients for LTD than for LTP induction at any given stimulus frequency. Cerebellar LTD depends on the activation of calcium/calmodulin-dependent kinase II (CaMKII). Using genetically modified (TT305/6VA and T305D) mice, we identified α-CaMKII inhibition upon autophosphorylation at Thr305/306 as a molecular event underlying the threshold shift. This mechanism enables frequency-independent plasticity control by the instructive CF signal based on relative, not absolute, calcium thresholds.
Positive Selection on the Osteoarthritis-Risk and Decreased-Height Associated Variants at the GDF5 Gene in East Asians

GDF5 is a member of the bone morphogenetic protein (BMP) gene family, and plays an important role in the development of the skeletal system. Variants of the gene are associated with osteoarthritis and height in some human populations. Here, we resequenced the gene in individuals from four geographically separated human populations, and found that the evolution of the promoter region deviated from neutral expectations, with the sequence evolution driven by positive selection in the East Asian population, especially the haplotypes carrying the derived alleles of 5′ UTR SNPs rs143384 and rs143383. The derived alleles of rs143384 and rs143383, which are associated with a risk of osteoarthritis and decreased height, have high frequencies in non-Africans and show strong extended haplotype homozygosity and high population differentiation in East Asian. It is concluded that positive selection has driven the rapid evolution of the two osteoarthritis osteoarthritis-risk and decreased height associated variants of the human GDF5 gene, and supports the suggestion that the reduction in body size during the terminal Pleistocene and Holocene period might have been an adaptive process influenced by genetic factors.
Assessment of the Risk of Venous Thromboembolism in Medical Inpatients using the Padua Prediction Score and Caprini Risk Assessment Model

Aim: The optimal risk assessment model (RAM) to stratify the risk of venous thromboembolism (VTE) in medical inpatients is not known. We examined and compared how well the Padua Prediction Score (PPS) and the Caprini RAM stratify VTE risk in medical inpatients. Methods: We undertook a retrospective case-control study among medical inpatients admitted to a large general hospital in China during a 4-year period. In total, 902 cases were confirmed to have VTE during hospitalization and 902 controls were selected randomly to match cases by medical service. Results: The VTE risk increased significantly with an increase of the cumulative PPS or Caprini RAM score. A PPS and Caprini RAM “high risk” classification was, respectively, associated with a 5.01-fold and 4.10-fold increased VTE risk. However, the Caprini RAM could identify 84.3% of the VTE cases to receive prophylaxis according to American College of Chest Physicians guidelines, whereas the PPS could only identify 49.1% of the VTE cases. In the medical inpatients studied, five risk factors seen more frequently in VTE cases than in controls in the Caprini RAM were not included in the PPS. The Caprini RAM risk levels were linked almost perfectly to in-hospital and 6-month mortality. Conclusions: Both the PPS and Caprini RAM can be used to stratify the VTE risk in medical inpatients effectively, but the Caprini RAM may be considered as the first choice in a general hospital because of its incorporation of comprehensive risk factors, higher sensitivity to identify patients who may benefit from prophylaxis, and potential for prediction of mortality.
Efficacy and Safety of Everolimus Plus Low‐Dose Tacrolimus Versus Mycophenolate Mofetil Plus Standard‐Dose Tacrolimus in De Novo Renal Transplant Recipients: 12‐Month Data

In this 12‐month, multicenter, randomized, open‐label, noninferiority study, de novo renal transplant recipients (RTxRs) were randomized (1:1) to receive everolimus plus low‐dose tacrolimus (EVR+LTac) or mycophenolate mofetil plus standard‐dose Tac (MMF+STac) with induction therapy (basiliximab or rabbit anti‐thymocyte globulin). Noninferiority of composite efficacy failure rate (treated biopsy‐proven acute rejection [tBPAR]/graft loss/death/loss to follow‐up) in EVR+LTac versus MMF+STac was missed by 1.4%, considering the noninferiority margin of 10% (24.6% vs. 20.4%; 4.2% [−3.0, 11.4]). Incidence of tBPAR (19.1% vs. 11.2%; p < 0.05) was significantly higher, while graft loss (1.3% vs. 3.9%; p < 0.05) and composite of graft loss/death/lost to follow‐up (6.1% vs. 10.5%, p = 0.05) were significantly lower in EVR+LTac versus MMF+STac groups, respectively. Mean estimated glomerular filtration rate was similar between EVR+LTac and MMF+STac groups (63.1 [22.0] vs. 63.1 [19.5] mL/min/1.73 m2) and safety was comparable. In conclusion, EVR+LTac missed noninferiority versus MMF+STac based on the 10% noninferiority margin. Further studies evaluating optimal immunosuppression for improved efficacy will guide appropriate dosing and target levels of EVR and LTac in RTxRs.