bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent Trends in the Near-Surface Climatology of the Northern North American Great Plains
Authors: Bromley Gabriel T. , Gerken Tobias , Prein Andreas F. , Stoy Paul C. 
Published: October 2019

AbstractWe examined climate trends in the northern North American Great Plains (NNAGP) from 1970 to 2015, a period that aligns with widespread land-use changes in this globally important agricultural region. Trends were calculated from the Climatic Research Unit (CRU) and other climate datasets using a linear regression model that accounts for temporal autocorrelation. The NNAGP warmed on an annual basis, with the largest change occurring in winter (DJF) at 0.4°C decade−1. January in particular warmed at nearly 0.9°C decade−1. The NNAGP cooled by −0.18°C decade−1 during May and June, nearly the opposite of global warming trends during the study period. The atmospheric vapor pressure deficit (VPD), which can limit crop growth, decreased in excess of −0.4 hPa decade−1 during climatological summer in the southeastern part of the study domain. Precipitation P increased in the eastern portion of the NNAGP during all seasons except fall and increased during May and June in excess of 8 mm decade−1. Climate trends in the NNAGP largely followed global trends except during the early warm season (May and June) during which 2-m air temperature Tair became cooler, VPD lower, and P greater across large parts of the study region. These changes are consistent with observed agricultural intensification during the study period, namely the reduction of summer fallow and expansion of agricultural land use. Global climate model simulations indicate that observed Tair trends cannot be explained by natural climate variability. However, further climate attribution experiments are necessary to understand if observed changes are caused by increased agricultural intensity or other factors.
Atmospheric Mixed Layer Convergence from Observed MJO Sea Surface Temperature Anomalies
Authors: de Szoeke Simon P. , Maloney Eric D. 
Published: October 2019

ABSTRACTThe Madden–Julian oscillation (MJO) dominates tropical weather on intraseasonal 30–90-day time scales, yet mechanisms for its generation, maintenance, and propagation remain unclear. Although surface moist static energy (MSE) flux is greatest under strong winds in the convective phase, sea surface temperature (SST) warms by ~0.3°C in the clear nonconvective phase of the MJO. Winds converging into the hydrostatic low pressure under warm air over the warm SST increase the vertically integrated MSE. We estimate column-integrated MSE convergence using a model of mixed layer (ML) winds balancing friction, planetary rotation, and hydrostatic pressure gradients. Small (0.3 K) SST anomalies associated with the MJO drive 7 W m−2net column MSE convergence averaged over the equatorial Indian Ocean ahead of MJO deep convection. The MSE convergence is in the right phase to contribute to MJO generation and propagation. It is on the order of the total MSE tendency previously assessed from reanalysis, and greater than surface heat flux anomalies driven by intraseasonal SST fluctuations.
Influence of Bottom Topography on Vortex Stability
Authors: Zhao Bowen , Chieusse-Gérard Emma , Flierl Glenn 
Published: October 2019

AbstractThe effects of topography on the linear stability of both barotropic vortices and two-layer, baroclinic vortices are examined by considering cylindrical topography and vortices with stepwise relative vorticity profiles in the quasigeostrophic approximation. Four vortex configurations are considered, classified by the number of relative vorticity steps in the horizontal and the number of layers in the vertical: barotropic one-step vortex (Rankine vortex), barotropic two-step vortex, and their two-layer, baroclinic counterparts with the vorticity steps in the upper layer. In the barotropic calculation, the vortex is destabilized by topography having an oppositely signed potential vorticity jump while stabilized by topography of same-signed jump, that is, anticyclones are destabilized by seamounts while stabilized by depressions. Further, topography of appropriate sign and magnitude can excite a mode-1 instability for a two-step vortex, especially relevant for topographic encounters of an otherwise stable vortex. The baroclinic calculation is in general consistent with the barotropic calculation except that the growth rate weakens and, for a two-step vortex, becomes less sensitive to topography (sign and magnitude) as baroclinicity increases. The smaller growth rate for a baroclinic vortex is consistent with previous findings that vortices with sufficient baroclinic structure could cross the topography relatively easily. Nonlinear contour dynamics simulations are conducted to confirm the linear stability analysis and to describe the subsequent evolution.
Sustained relief of trigeminal neuropathic pain by a blood–brain barrier penetrable PPAR gamma agonist
Authors: Zhang Morgan , Hu Min , Montera Marena A , Westlund Karin N 
Published: October 2019

The blood–brain barrier (BBB) and blood–nerve barrier ensure protection of the nervous system but pose a challenge for the treatment of pain since it restricts passage of many therapeutic drugs. Although it is unknown which blood–neural barrier is more relevant, or whether permeabilities are the same for different barriers, we proposed that the inefficiency of thiazolidinedione-type agonists for peroxisome proliferator-activated receptor gamma (PPARɣ) is due to their difficulty in passage through the BBB. We developed a new highly BBB penetrable PPARɣ agonist for the treatment of neuropathic pain, assuming BBB permeability is a rule of thumb to estimate the overall permeability of relevant blood–neural barriers. As an index of brain penetration, the brain–plasma ratio (Kp) of ELB00824 is 5.13, suggesting very high brain bioavailability, which is 58-fold that of pioglitazone. The series of studies presented here indicate that ELB00824 may be the most potent PPARɣ agonist currently known for acute reduction of neuropathic pain in trigeminal nerve in rat and mouse models. Low-dose PPARɣ agonist, ELB00824 (10 mg/kg), effectively decreased neuropathic hypersensitivity in mice and rats at both acute and chronic time points, a dose 100-fold lower than the effective dose (1000 mg/kg, i.p.) of pioglitazone. Comparisons of ELB00824 alone or in combination with gabapentin or carbamazepine are provided. While PPARɣ agonists used to treat Type 2 diabetes produce several adverse side effects, sub-chronic oral toxicity study provided promising results that ELB00824 does not produce any significant short-term toxicity. The study animals of either sex remained alive and healthy with no significant alteration of body weight long term. Toxicity study results obtained were satisfactory, with no significant alterations in any serum biochemistry parameters.
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU
Authors: Fang Chih-Hao , Theera-Ampornpunt Nawanol , Roth Michael A. , Grama Ananth , Chaterji Somali 
Published: October 2019

AbstractBackgroundThe data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional annotation problem, within the bounds of the hardware constraints and the model’s complexity. In our systemAikyatan, we annotate distal epigenomic regulatory sites, e.g., enhancers. Specifically, we develop a binary classifier that classifies genome sequences as distal regulatory regions or not, given their histone modifications’ combinatorial signatures. This problem is challenging because the regulatory regions are distal to the genes, with diverse signatures across classes (e.g., enhancers and insulators) and even within each class (e.g., different enhancer sub-classes).ResultsWe develop a suite of ML models, under the bannerAikyatan, including SVM models, random forest variants, and deep learning architectures, for distal regulatory element (DRE) detection. We demonstrate, with strong empirical evidence, deep learning approaches have a computational advantage. Plus, convolutional neural networks (CNN) provide the best-in-class accuracy, superior to the vanilla variant. With the human embryonic cell line H1, CNN achieves an accuracy of 97.9% and an order of magnitude lower runtime than the kernel SVM. Running on a GPU, the training time is sped up 21x and 30x (over CPU) for DNN and CNN, respectively. Finally, our CNN model enjoys superior prediction performance vis-‘a-vis the competition. Specifically,Aikyatan-CNN achieved 40% higher validation rate versus CSIANN and the same accuracy as RFECS.ConclusionsOur exhaustive experiments using an array of ML tools validate the need for a model that is not only expressive but can scale with increasing data volumes and diversity. In addition, a subset of these datasets have image-like properties and benefit from spatial pooling of features. OurAikyatansuite leverages diverse epigenomic datasets that can then be modeled using CNNs with optimized activation and pooling functions. The goal is to capture the salient features of the integrated epigenomic datasets for deciphering the distal (non-coding) regulatory elements, which have been found to be associated with functional variants. Our source code will be made publicly available at:https://bitbucket.org/cellsandmachines/aikyatan.
Prevalence of first-degree atrioventricular block and the associated risk factors: a cross-sectional study in rural Northeast China
Authors: Du Zhi , Xing Liying , Lin Min , Tian Yuanmeng , Jing Li , Yan Han , Zhang Boqiang , Liu Shuang , Yu Shiwen , Sun Yingxian 
Published: October 2019

Abstract

Background
First-degree atrioventricular block (AVB) has traditionally been regarded as a benign condition but recent studies have challenged this conception. Prevalence of 1–2% have been reported in developed countries in Asia. However, no epidemiologic studies have established the prevalence of first-degree AVB in developing countries. The aim of the study was to investigate the prevalence of first-degree AVB in rural northeast China and identify the associated risk factors.

Methods
This cross-sectional study was undertaken from September 2017 to May 2018 in rural areas of Liaoning Province. It involved 10,926 participants aged ≥40 years (85.3% of those who were eligible). First-degree AVB was confirmed by at least two independent cardiologists. Risk factors were evaluated using stepwise logistic regression.

Results
The prevalence of first-degree AVB was 3.4% (95% confidence interval [CI]: 3.0–3.8%). Males had a higher prevalence than females (5.1% vs. 2.2%, p < 0.001). The regression model involving all participants showed that age (odds ratio [OR]: 1.32; p <0.001), male sex (OR: 1.72; p = 0.001), height (OR: 1.25; p = 0.008), systolic blood pressure (SBP) (OR: 1.15; p = 0.003), triglycerides (TG) (OR: 1.10; p < 0.001), high-density lipoprotein cholesterol (HDL-C) (OR: 0.73; p < 0.001), heart rate (OR: 0.78; p < 0.001), and exercising regularly (OR: 0.73; p = 0.030) were independent risk factors.

Conclusions
First-degree AVB is highly prevalent in rural areas of northeast China. The associated independent risk factors include being male, older, and taller, higher SBP and TG, lower HDL-C and heart rate, and lack of exercise.
Braden scale for assessing pneumonia after acute ischaemic stroke
Authors: Ding Yunlong , Yan Yazhou , Niu Jiali , Zhang Yanrong , Gu Zhiqun , Tang Ping , Liu Yan 
Published: October 2019

Abstract

Background
The prevention of pneumonia is critical for patients with acute ischaemic stroke (AIS). The six subscales in the Braden Scale seem to be related to the occurrence of pneumonia. We aimed to evaluate the feasibility of using the Braden Scale to predict the occurrence of pneumonia after AIS.

Methods
We studied a series of consecutive patients with AIS who were admitted to the hospital. The cohort was subdivided into pneumonia and no pneumonia groups. The scores on the Braden Scale, demographic characteristics and clinical characteristics were obtained and analysed by statistical comparisons between the two groups. We investigated the predictive validity of the Braden Scale by receiver operating characteristic (ROC) curve analysis.

Results
A total of 414 patients with AIS were included in this study. Of those 414 patients, 57 (13.8%) patients fulfilled the criteria for post-stroke pneumonia. There were significant differences in age and histories of chronic obstructive pulmonary disease (COPD), dysphagia and Glasgow Coma Scale (GCS) score between the two groups, and the National Institutes of Health Stroke Scale (NIHSS) score in the pneumonia group was significantly higher than that in the no pneumonia group (P < 0.01). The mean score on the Braden Scale in the pneumonia group was significantly lower than that in the no pneumonia group (P < 0.01). The six subscale scores on the Braden Scale were all significantly different between the two groups. The area under the curve (AUC) for the Braden Scale for the prediction of pneumonia after AIS was 0.883 (95% CI = 0.828–0.937). With 18 points as the cutoff point, the sensitivity was 83.2%, and the specificity was 84.2%.

Conclusion
The Braden Scale with 18 points as the cutoff point is likely a valid clinical grading scale for predicting pneumonia after AIS at presentation. Further studies on the association of the Braden Scale score with stroke outcomes are needed.
Multiple sequence types responsible for healthcare-associated Acinetobacter baumannii dissemination in a single centre in Egypt
Authors: Al-Hassan Leena , Zafer Mai M. , El-Mahallawy Hadir 
Published: October 2019

Abstract

Background
Acinetobacter baumannii is an increasingly worrying organism in the healthcare setting, due to its multidrug resistance and persistence. Prolonged hospitalisation, immunocompromised patients and excessive antibiotic exposure all contribute to increasing the risk of A. baumannii infections, which makes cancer patients a significant risk group. This study aims to investigate the dissemination of A. baumannii at the National Cancer Institute (NCI) in Cairo – Egypt.

Methods
All bacterial isolates were typed using Multi-locus Sequence Typing (MLST) to characterise the epidemiology of isolates. The intrinsic OXA-51-like, and the acquired carbapanemases OXA-23, − 24/40, − 58, NDM, IMP, and VIM were also amplified and sequenced to genetically identify mechanisms of carbapenem resistance.

Results
MLST results show a high degree of multi-clonal dissemination, with 18 different Sequence Types (STs) identified, including 5 novel. The majority of isolates belonged to International Clone (IC) 2, and carbapenem resistance was detected in 93% of isolates and mediated by blaOXA-23, blaOXA-58, blaNDM-1 and blaVIM-1. We also report the presence of a resistant ST732 (OXA-378) which has been previously identified in migratory birds.

Conclusions
Multiple highly resistant clones were identified in a Cancer hospital in Cairo. It is vital that clinicians and healthcare workers are aware of the population of A. baumannii present in order to have appropriate treatment and infection control practices.
Past history of stage I/II solid tumor malignancy impacts considerably on sepsis mortality: a propensity score matching analysis from the hellenic sepsis study group
Authors:   on behalf of the Hellenic Sepsis Study Group, Dimοpoulos George , Rovina Nikoletta , Patrani Maria , Antoniadou Eleni , Konstantonis Dimitrios , Vryza Konstantina , Vlachogianni Glykeria , Kyprianou Miltiades , Routsi Christina , Giamarellos-Bourboulis Evangelos J. 
Published: October 2019

Abstract

Background
Whether past history of solid stage I/II inactive cancer has an impact on 28-day mortality of sepsis remains unclear. We aimed to determine the impact of history of stage I or II solid tumor malignancy in complete remission the last 3 years on sepsis outcome.

Methods
Using the database of the Hellenic Sepsis Study Group from 1553 patients with sepsis admitted in the ICU, 83 patients with sepsis by Sepsis-3 definition with past-history of stage I/II inactive solid malignancy the last 3 years were depicted. A comparator group of 83 patients fully matched for age, severity, type of infection and comorbidities was selected by propensity score matching.

Results
Mortality after 28 days was 37.3% in the comparator group and 54.2% in the solid tumor stage I/II group (odds ratio for death 1.98; p: 0.030). Following step-wise forward Cox regression analysis, septic shock (hazard ratio 1.80), acute renal injury (hazard ratio 2.06), history of coronary heart disease (hazard ratio 0.36) and history of stage I/II solid tumor malignancy (hazard ratio 1.79) were the only independent variables associated with 28-day mortality. Serum levels of procalcitonin and of soluble urokinase plasminogen activator receptor were similar between the two groups of comparisons.

Conclusions
Past history of stage I/II solid malignancy is an independent risk factor for unfavorable outcome from sepsis the first 28 days.
Adiponectin levels in maternal serum and umbilical cord blood at birth by mode of delivery: relationship to anthropometric measurements and fetal sex
Authors: Fazeli Daryasari Seyedeh Razieh , Tehranian Najmeh , Kazemnejad Anoshirvan , Razavinia Fatemeh , Tork Tatari Fatemeh , Pahlavan Fattaneh 
Published: October 2019

Abstract

Background
The rate of cesarean section is increasing worldwide. Adiponectin is a hormone related to anti-inflammatory and anti-atherogenic effects; and it′s concentrations may change in response to inflammatory situations including surgical intervention. The aim of the current study was to investigate serum adiponectin levels in maternal and umbilical cord blood according to different modes of delivery and their relationship with anthropometric measurements and fetal sex.

Methods
The study population initially comprised 90 healthy pregnant women referred to the teaching hospital. Eventually, 40 participants in the vaginal delivery group and 35 subjects in the cesarean delivery group were recruited in to the study. Umbilical cord blood and maternal serum samples were analyzed according to the standard protocol from the manufacturer. The collected data were analyzed using SPSS-16 software. P-value < 0.05 was considered as the significance level for all tests.

Results
Our results indicated a significant association between maternal adiponectin and the mode of delivery, with adiponectin levels significantly higher in vaginal delivery compared to cesarean section (P < 0.001). However, no difference was found in umbilical cord blood adiponectin between the two groups (P = 0.51). A significant positive correlation was found between maternal serum adiponectin in the first day after birth and umbilical cord blood adiponectin in the vaginal delivery group (P = 0.007). Nevertheless, this correlation was not statistically significant in the cesarean delivery group (P = 0.62). There was also no significant correlation between fetal sex and anthropometric measurements with maternal adiponectin (P = 0.44) and umbilical cord blood adiponectin (P = 0.86).

Conclusions
The result of the current study revealed that maternal adiponectin concentration was significantly higher in vaginal delivery compared to cesarean section, which might be due to the increased levels of maternal adiponectin release during labor.
The effects of photodynamic therapy on leukemia cells mediated by KillerRed, a genetically encoded fluorescent protein photosensitizer
Authors: Yuan Meng , Liu Chengcheng , Li Jiao , Ma Wenpeng , Yu Xiaozhuo , Zhang Ping , Ji Yanhong 
Published: October 2019

AbstractBackgroundLeukemia is a cancer of blood and bone marrow cells, causing about 300,000 deaths worldwide. Photodynamic therapy (PDT) is a promising alternative for the treatment of malignant tumors. KillerRed is a genetically encoded red fluorescent protein photosensitizer (PS). In this study, we aimed to investigate the effects of KillerRed-mediated PDT on chronic myelogenous leukemia K562 cells, acute monocytic leukemia NB4 cells, and acute monocytic leukemia THP1 cells.MethodsKillerRed was expressed inEscherichia colicells, purified by Q-Sepharose column, and confirmed by western-blotting. The PDT effect on cell proliferation was evaluated by Cell Counting Kit-8 (CCK-8). Cell apoptosis was determined by PE Annexin V/7-AAD staining and flow cytometry. The distribution of KillerRed in leukemia cells was detected by confocal laser scanning microscopy (CLSM) and western-blotting. The ROS generation was measured by flow cytometry.ResultsPure KillerRed was obtained with a yield of about 37 mg per liter of bacterial cells. KillerRed photodynamic inactivated the leukemia cells in a concentration-dependent manner, but exhibited no obvious dark toxicity. PDT mediated by KillerRed could also induce apoptotic response (mainly early apoptosis) in the three cell lines. The CLSM imaging indicated that KillerRed was distributed within the cytoplasm and nuclei of leukemia cells, causing damages to the cytoplasm and leaving the nuclear envelope intact during light irradiation. KillerRed distributed both in the cytosol and nuclei was confirmed by western blotting, and ROS significantly increased in PDT treated cells compared to the cells treated with KillerRed alone.ConclusionsOur studies demonstrated that KillerRed-mediated PDT could effectively inactivate K562, NB4, and THP1 leukemia cells and trigger cell apoptosis, and it has potential to be used individually or complementally, in the treatment of leukemia.
Adherence and barriers to penile rehabilitation over 2 years following radical prostatectomy
Authors: Albaugh Jeffrey , Adamic Brittany , Chang Cecilia , Kirwen Nicholas , Aizen Joshua 
Published: October 2019

Abstract

Background
A variety of penile rehabilitation (PR) therapies are available to improve post-prostatectomy erectile dysfunction (ED) with mixed results. It is uncertain how adherent men are to PR therapies. The aim of this study is to determine adherence to and identify barriers to PR treatment.

Methods
A longitudinal cross-sectional approach was used in men who underwent radical prostatectomy over 2 years. Men were instructed to take a PDE5 inhibitor (PDE5i) three times per week, and if required, utilize a vacuum constriction device (VCD) daily. Outcomes were measured by multiple validated questionnaires. In addition, penile stretched length, side effects, compliance to PR regimen & barriers to participation were documented.

Results
Seventy-seven patients were enrolled, however only 49 completed evaluation at 3 or more timepoints and were included in analysis. This cohort was an average age of 58.1 years (±7.7), had robotic laparoscopic radical prostatectomy (91.7%), and had bilateral nerve sparing procedures (95.8%). Majority (62.5%) reported normal SHIM pre-operatively, however 79% used PDE5i. Erectile function as measured by IIEF and Erection Hardness Rating were negatively affected post-operatively, with gradual improvement in parameters throughout the 24 month follow up. Of the participants who had normal pre-op SHIM, only 23.1 and 28.6% regained baseline function at 1 and 2 years, respectively. Orgasm was significantly diminished immediately post-operatively, however, at the end of the study period only 37% of men reported diminished climax and no men reported absent orgasm. Adherence to penile rehabilitation therapies declined overtime. Men took oral PDE5i on average 2.3 times weekly at 12 and 24 months (p < 0.001). Men used the VCD 2.3–3.9 days a week, which declined overtime (p = 0.014).

Conclusions
Improvement in erectile and orgasm parameters was observed over time, but most men did not return to baseline function. Despite comprehensive instructions and a frequent follow up schedule, PDE5i and VCD adherence was poor. High attrition rates were noted with only 55.8% of men remaining at 12 months and 45% of men completing 24 months. The most common barriers to PR adherence were cost, inconvenience and perceived ineffectiveness.