bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptides derived from the HIV-1 integrase promote HIV-1 infection and multi-integration of viral cDNA in LEDGF/p75-knockdown cells
Authors: Levin Aviad , Hayouka Zvi , Friedler Assaf , Loyter Abraham 
Published: December 2019

AbstractBackgroundThe presence of the cellular Lens Epithelium Derived Growth Factor p75 (LEDGF/p75) protein is essential for integration of the Human immunodeficiency virus type 1 (HIV-1) cDNA and for efficient virus production. In the absence of LEDGF/p75 very little integration and virus production can be detected, as was demonstrated using LEDGF/p75-knokdown cells.ResultsHere we show that the failure to infect LEDGF/p75-knockdown cells has another reason aside from the lack of LEDGF/p75. It is also due to inhibition of the viral integrase (IN) enzymatic activity by an early expressed viral Rev protein. The formation of an inhibitory Rev-IN complex in virus-infected cells can be disrupted by the addition of three IN-derived, cell-permeable peptides, designated INr (IN derived-Rev interacting peptides) and INS (IN derived-integrase stimulatory peptide). The results of the present work confirm previous results showing that HIV-1 fails to infect LEDGF/p75-knockdown cells. However, in the presence of INrs and INS peptides, relatively high levels of viral cDNA integration as well as productive virus infection were obtained following infection by a wild type (WT) HIV-1 of LEDGF/p75-knockdown cells.ConclusionsIt appears that the lack of integration observed in HIV-1 infected LEDGF/p75-knockdown cells is due mainly to the inhibitory effect of Rev following the formation of a Rev-IN complex. Disruption of this inhibitory complex leads to productive infection in those cells.
Gravitation field algorithm and its application in gene cluster
Authors: Zheng Ming , Liu Gui-xia , Zhou Chun-guang , Liang Yan-chun , Wang Yan 
Published: December 2019

Abstract

Background
Searching optima is one of the most challenging tasks in clustering genes from available experimental data or given functions. SA, GA, PSO and other similar efficient global optimization methods are used by biotechnologists. All these algorithms are based on the imitation of natural phenomena.

Results
This paper proposes a novel searching optimization algorithm called Gravitation Field Algorithm (GFA) which is derived from the famous astronomy theory Solar Nebular Disk Model (SNDM) of planetary formation. GFA simulates the Gravitation field and outperforms GA and SA in some multimodal functions optimization problem. And GFA also can be used in the forms of unimodal functions. GFA clusters the dataset well from the Gene Expression Omnibus.

Conclusions
The mathematical proof demonstrates that GFA could be convergent in the global optimum by probability 1 in three conditions for one independent variable mass functions. In addition to these results, the fundamental optimization concept in this paper is used to analyze how SA and GA affect the global search and the inherent defects in SA and GA. Some results and source code (in Matlab) are publicly available at http://ccst.jlu.edu.cn/CSBG/GFA.
Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers
Authors: Liu Xiaoping , Liu Rui , Zhao Xing-Ming , Chen Luonan 
Published: December 2019

Abstract

Background
Type 1 diabetes (T1D) is a complex disease and harmful to human health, and most of the existing biomarkers are mainly to measure the disease phenotype after the disease onset (or drastic deterioration). Until now, there is no effective biomarker which can predict the upcoming disease (or pre-disease state) before disease onset or disease deterioration. Further, the detail molecular mechanism for such deterioration of the disease, e.g., driver genes or causal network of the disease, is still unclear.

Methods
In this study, we detected early-warning signals of T1D and its leading biomolecular networks based on serial gene expression profiles of NOD (non-obese diabetic) mice by identifying a new type of biomarker, i.e., dynamical network biomarker (DNB) which forms a specific module for marking the time period just before the drastic deterioration of T1D.

Results
Two dynamical network biomarkers were obtained to signal the emergence of two critical deteriorations for the disease, and could be used to predict the upcoming sudden changes during the disease progression. We found that the two critical transitions led to peri-insulitis and hyperglycemia in NOD mices, which are consistent with other independent experimental results from literature.

Conclusions
The identified dynamical network biomarkers can be used to detect the early-warning signals of T1D and predict upcoming disease onset before the drastic deterioration. In addition, we also demonstrated that the leading biomolecular networks are causally related to the initiation and progression of T1D, and provided the biological insight into the molecular mechanism of T1D. Experimental data from literature and functional analysis on DNBs validated the computational results.
Isolated zone I vertical fracture of first sacral vertebra: a case report
Authors: Bilgic Serkan , Kilincoglu Volkan , Yurttas Yüksel , Soylu Kenan , Sehirlioglu Ali 
Published: December 2019

AbstractIsolated sacral fractures which occur by shear forces on the pelvic ring are seen less commonly and they are commonly transversely oriented. A 29-year-old Turkish female patient, who sat in front seat in the car, was unrestrained, and another car hit them from right front side of their vehicle. Physical examination revealed considerable tenderness over the right superior gluteal region and excruciating pain during sacral and iliac compression. There was no clear fracture line in her plain radiographs. CT revealed incomplete, zone I fracture located on the superior and anterior part of the first sacral vertebra. Type 1 lateral compression pelvic fractures are relatively common and they include impacted sacral and ipsilateral rami fractures. Only a few cases, related with the isolated sacral fracture, have been reported in the literature. To our knowledge, no isolated vertical zone I fracture of the first sacral vertebra which occurred with the lateral compression injury has been described previously. Fracture of the sacrum should be suspected in the presence of sacral pain and tenderness.
Voice estimation in patients after reconstructive subtotal laryngectomy
Authors: Wiskirska-Woźnica Bożena , Leszczyńska Małgorzata , Świdziński  , Czerniejewska Hanna , Jackowska Joanna , Witold Szyfter 
Published: December 2019

AbstractBackgroundTreatment of laryngeal cancers, may include surgery, radiotherapy, chemotherapy, or a combination. Total laryngectomy (TL) has been the standard surgical treatment. Partial laryngectomy procedures were performed, their advantage over TL is preservation of laryngeal functions.MethodsThe investigation was carried out on a group of 20 patients (3 female and 17 male), who underwent surgery according the techniques mentioned above. The methods of investigation were based on perceptual voice estimation (GRBAS), videolaryngostroboscopy, acoustic voice analysis, aerodynamic measure maximum phonation time, voice self-assessment (VHI).Results and ConclusionsThe perceptual voice estimation revealed a good phonation result in only 3 cases after using surgery with the Calearo method as well as the best results of MPT. The VHI reflected severe voice handicap in 2 patients (26 to 40 points). No statistically significant differences were observed between the values of the acoustic parameters in MDVP analysis after following operation -CHEP, Calearo, Sedlacek.
Reproductive phenology and pre-dispersal fruit predation in Atriplex halimus L. (Chenopodiaceae)
Authors: Romera Prado , Fernández-Illescas Francisca , Nieva F Javier J , Rodríguez-Rubio Pilar , Sánchez-Gullón Enrique , Muñoz-Rodríguez Adolfo F 
Published: December 2019

Abstract

Background
The flowering phenology pattern of Atriplex halimus was studied in a Mediterranean habitat in order to analyze protandry effectiveness. Fruit set evolution was recorded over two years and the impact of pre-dispersal predation by insects was also evaluated.

Results
The flowering phenology coincided in 2006 and 2007, starting in mid-July and reaching full flowering at the end of August in both years. Inflorescences are composed of glomerules with 8.78 ± 2.79 male flowers and 4.57 ± 2.58 female flowers, with no significant differences in position on the inflorescence. The peaks of male and female flower anthesis were reached in mid-August, but the male maximum occurred one week before the female. Plants at the start of flowering only bear male flowers, but female flowers soon appear. Fruit set starts at the end of August; all the flowers were transformed into fruit by mid-September and their development continued to the beginning of October, when fruit structures had matured and began to drop. Fruit predation started at the end of September and reached maximum intensity in mid-October.

Conclusions
At population level, male and female flowers seemed to open in the same weeks, but at plant and glomerule level male flowers opened one week before the females. Fruit predation levels were 62.42 and 43.14% in 2006 and 2007 respectively, with no significant differences between different parts of the inflorescence. And larvae of Coleophoridae were the most abundant predators.
Intra-abdominal pressure measurement using the FoleyManometer does not increase the risk for urinary tract infection in critically ill patients
Authors: Desie Nele , Willems Alexandra , De laet Inneke , Dits Hilde , Van Regenmortel Niels , Schoonheydt Karen , Van De Vyvere Martine , Malbrain Manu LNG 
Published: December 2019

Abstract

Objective
The aim of this study was to determine whether intra-abdominal pressure (IAP) monitoring using the FoleyManometer (Holtech Medical, Charlottenlund, Denmark) increases the risk of urinary tract infection (UTI).

Design
A retrospective database review was conducted.

Setting
The study was conducted in the 12-bed medical intensive care unit of ZNA Stuivenberg Hospital (Antwerp, Belgium), a tertiary hospital.

Patients
There were 5,890 patients admitted to the medical intensive care unit of which 1,097 patients underwent intrabladder pressure (IBP) monitoring as estimate for IAP.

Interventions
Crude and adjusted UTI rates were compared among patients undergoing IAP measurements with three different intrabladder methods: a modified homemade technique, a FoleyManometer with 35 ml reservoir, and a FoleyManometer low volume (FoleyManometerLV) with less than 10 ml priming volume.

Measurements and results
Four consecutive time periods of 24 months were defined and compared with regard to IAP measurement: period 1 (2000-2001), during which IAP monitoring was not used routinely (which serves as a control group), was compared with period 2 (2002-2003), using a modified homemade technique; period 3 (2004-2005), introducing the FoleyManometer; and finally period 4 (2006-2007), in which the FoleyManometerLV was introduced. The incidence of IBP measurements increased from 1.4% in period 1 to 45.4% in period 4 (p < 0.001). At the same time, the Simplified Acute Physiology Score (version 2) (SAPS-II) increased significantly from 24.4 ± 21.5 to 34.9 ± 18.7 (p < 0.001) together with the percentage of ventilated patients from 18.6% to 40.7% (p < 0.001). In total, 1,097 patients had IAP measurements via the bladder. The UTI rates were adjusted for disease severity by multiplying each crude rate with the ratio of control versus study patient SAPS-II probability of mortality. Crude and adjusted UTI rates per 1,000 catheter days (CD) were on average 16.1 and 12.8/1,000 CD, respectively, and were not significantly different between the four time periods.

Conclusions
Intrabladder pressure monitoring as estimate for IAP either via a closed transducer technique or the closed FoleyManometer technique seems safe and does not alter the risk of UTI in critically ill patients.
Climate change impacts on Ontario wind power resource
Authors: Yao Yao , Huang Gordon H , Lin Qianguo 
Published: December 2019

Abstract

Background
The availability and reliability of wind power depend largely on current and future climate conditions, which may vary in the context of climate change. A high resolution regional climate model (PRECIS) was used for dynamic downscaling of the future wind speed over Ontario. The changes of wind power density and power production were further investigated through case studies.

Results
The spatial pattern and the magnitude of wind speed from PRECIS simulation, Wind Energy Atlas and the observation indicated a successful climate simulation. Climate modelling indicated that there would be a decrease of up to 5% in wind speed over southern Ontario from present to the period of 2071–2100. It was showed in the case studies that the changes of wind power production were not in proportion to the changes of average wind speed, due to the variations of wind speed distribution.

Conclusion
The decrease of projected wind speed would be more intense in A2 than in B2 scenario, showing statistically significant differences in the grid cell mean wind speed. The changes of wind power production may not be in proportion to the changes of average wind speed. It would be reasonable to develop onshore or offshore wind energy industry around Georgian Bay and James Bay, considering the projected increasing wind speeds within these areas.
Aripiprazole as augmentation therapy in bipolar patients with current minor or subsyndromal mood symptoms
Authors: Schweitzer Isaac , Sarris Jerome , Tuckwell Virginia , Maguire Kay , Smith Deidre , Ng Chee 
Published: December 2019

Abstract

Background
This study aims to evaluate the effectiveness of aripiprazole augmentation of maintenance treatment for bipolar disorder in patients with minor or subsyndromal mood episodes while on a stable dose of a mood stabiliser and/or antidepressant.

Methods
All subjects had a diagnosis of bipolar I or II disorder (Diagnostic and Statistical Manual of Mental Disorders-4th Edition, Text Revision). Open-label aripiprazole was given over 8 weeks initially. The starting dose was 5 to 15 mg/day with a mean final dose of 11.5 mg (±4.6). Patients were assessed at weeks 0, 2, 4 and 8 with the Montgomery-Asberg Depression Rating Scale (MADRS), Young Mania Rating Scale (YMRS) and Clinical Global Impression of Severity (CGI-S).

Results and discussion
Seventeen of 20 (85%) patients completed week 4, while 14 (70%) patients completed 8 weeks. For intention-to-treat data, there was a significant decrease in MADRS scores over the course of treatment, with a reduction of 6.40 points at endpoint (p < 0.0005). Improvement from baseline was significant at week 2 and remained through to week 8. Similarly, CGI-S scores significantly decreased over the course of study, but not YMRS scores. Aripiprazole was shown to be a modestly effective augmentation therapy for depressive symptoms in bipolar I and II in this small open-label study.
Re-tooling critical care to become a better intensivist: something old and something new
Authors: Marini John J 
Published: December 2019

AbstractDevelopments in recent years have placed powerful new tools of diagnosis, therapy, and communication at the disposal of medicine in general, and of critical care in particular. The art of healing requires not only technical proficiency, but also personal connection, multidisciplinary teamwork, and commitment to the venerable traditions of our profession. The latter often seem to be under assault by today's high-pressure, high-efficiency, and increasingly business-driven hospital environments. Re-tooling critical care for the future generations of caregivers requires something old--empathetic connection--as well as the exciting newer technologies of our science and practice.
Advances in the support of respiratory failure: putting all the evidence together
Authors: Marini John J 
Published: December 2019

AbstractConsiderable progress has been made recently in the understanding of how best to accomplish safe and effective ventilation of patients with acute lung injury. Mechanical and nonmechanical factors contribute to causation of ventilator-associated lung injury. Intervention timing helps determine the therapeutic efficacy and outcome, and the stage and severity of the disease process may determine the patient's vulnerability as well as an intervention's value. Reducing oxygen consumption and ventilatory demands are key to a successful strategy for respiratory support of acute respiratory distress syndrome. Results from major clinical trials can be understood against the background of the complex physiology of ventilator-induced lung injury.
Winning the war against ICU-acquired weakness: new innovations in nutrition and exercise physiology
Authors: Wischmeyer Paul E , San-Millan Inigo 
Published: December 2019

AbstractOver the last 10 years we have significantly reduced hospital mortality from sepsis and critical illness. However, the evidence reveals that over the same period we have tripled the number of patients being sent to rehabilitation settings. Further, given that as many as half of the deaths in the first year following ICU admission occur post ICU discharge, it is unclear how many of these patients ever returned home. For those who do survive, the latest data indicate that 50-70% of ICU "survivors" will suffer cognitive impairment and 60-80% of "survivors" will suffer functional impairment or ICU-acquired weakness (ICU-AW). These observations demand that we as intensive care providers ask the following questions: "Are we creating survivors ... or are we creating victims?" and "Do we accomplish 'Pyrrhic Victories' in the ICU?" Interventions to address ICU-AW must have a renewed focus on optimal nutrition, anabolic/anticatabolic strategies, and in the future employ the personalized muscle and exercise evaluation techniques utilized by elite athletes to optimize performance. Specifically, strategies must include optimal protein delivery (1.2-2.0 g/kg/day), as an athlete would routinely employ. However, as is clear in elite sports performance, optimal nutrition is fundamental but alone is often not enough. We know burn patients can remain catabolic for 2 years post burn; thus, anticatabolic agents (i.e., beta-blockers) and anabolic agents (i.e., oxandrolone) will probably also be essential. In the near future, evaluation techniques such as assessing lean body mass at the bedside using ultrasound to determine nutritional status and ultrasound-measured muscle glycogen as a marker of muscle injury and recovery could be utilized to help find the transition from the acute phase of critical illness to the recovery phase. Finally, exercise physiology testing that evaluates muscle substrate utilization during exercise can be used to diagnose muscle mitochondrial dysfunction and to guide a personalized ideal heart rate, assisting in recovery of muscle mitochondrial function and functional endurance post ICU. In the end, future ICU-AW research must focus on using a combination of modern performance-enhancing nutrition, anticatabolic/anabolic interventions, and muscle/exercise testing so we can begin to create more "survivors" and fewer victims post ICU care.
Physiology versus evidence-based guidance for critical care practice
Authors: Gattinoni Luciano , Carlesso Eleonora , Santini Alessandro 
Published: December 2019

AbstractEvidence based medicine is an attempt to optimize the medical decision process through methods primarily based on evidence coming from meta-analyses, systematic reviews, and randomized controlled trials ("evidence-based medicine"), rather than on "clinical judgment" alone. The randomized trials are the cornerstones of this process. However, the randomized trials are just a method to prove or disprove a given hypothesis, which, in turn, derives from a general observation of the reality (premises or theories). In this paper we will examine some of the most recent randomized trials performed in Intensive Care, analyzing their premises, hypothesis and outcome. It is quite evident that when the premises are wrong or too vague the unavoidable consequences will be a negative outcome. We should pay when designing the trial an equal attention in defining premises and hypothesis that we pay for the trial conduction.
Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Authors: Ranjard Louis , Wong Thomas K. F. , Rodrigo Allen G. 
Published: December 2019

Abstract
Background
In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging.

Results
Here, we introduce a new algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences.

Conclusions
We introduced an algorithm to perform dynamic alignment of reads on a distant reference. We showed that such approach can improve the reconstruction of an amplicon compared to classically used bioinformatic pipelines. Although not portable to genomic scale in the current form, we suggested several improvements to be investigated to make this method more flexible and allow dynamic alignment to be used for large genome assemblies.