bluuebunny/crossref_metadata_2025 huggingface dataset:
Completion Design Optimization for Unconventional Wells Using Large Scale Computational Science
Authors: Cotrell David , Hoeink Tobias , Odusina Elijah , Ghorpade Sachin , Stolyarov Sergey
Published: October 2019

In the current state of the oil and gas industry, unconventional resources are a significant source of the total production output. Unconventional wells remain profitable at various price points, because initial stimulation treatments can be tailored to changing market conditions, reflecting completion costs and (estimated) hydrocarbon prices. The same holds true for re-stimulation of already producing wells. Stimulation treatment "opens" up the subsurface to ultimately allow for better drainage of the reservoir hydrocarbons. The primary stimulation treatment currently in use is hydraulic fracturing, in which the wellbore is broken up into multiple stages, and highly pressurized fluid (oftentimes water) is pumped into each stage of the wellbore. This causes fractures to propagate away from the wellbore, which in turn enhances the local reservoir permeability and allows for economical production. Historically, the number of stages, and clusters per stage, for hydraulic stimulation has been based on wellbore horizontal length (e.g., 200 ft or 400 ft), or much valued previous experience in the same or similar area, as well as other investment considerations. Over time, a strong tendency has developed to place stages and clusters closer together to improve production. However, it is reasonable to assume that there will be a point beyond which adding another stage becomes more expensive than what is gained by increased production revenue from the greater stage count (i.e., less profitable depending on the time of investment). This scenario frames a classic optimization problem which is solved using Monte Carlo methods. Results show that optimal stimulation treatment configurations are robust for many objective functions related to the fracturing process (e.g., propped length and propped height). However, we find that objective functions related to production, production revenue, and profit often provide different optimum treatment configurations, and that those optima shift with respect to the considered timeframe. Because business decisions will ultimately be based on profit decisions over a given time span, we propose utilizing the appropriate objective function together with an integrated modeling approach such as presented here.
Improving the Effectiveness of Multi-Stage Hydraulic Fracturing in Horizontal Wells by Fracture Height Restriction
Authors: Valiullin Albert , Astafyev Vladimir , Osipov Ilya
Published: October 2019

The cost-effective development of low-permeability hydrocarbon formations of small thickness requires horizontal wells with multi-stage hydraulic fracturing (MS-Frac). The presence of higher or lower layers that are water-saturated and weak barriers to height growth imposes a restriction on the desirable geometry of the fracture to prevent a breakthrough into a flooded interval. Combining several methods of fracture height restriction and controlling such height can improve the efficiency of multi-stage hydraulic fracturing. The first technology to control the effective pressure was based on changing fracturing fluid rheology and resulted in a decrease in the net pressure and the fracture height. The main treatment buffer utilized a hybrid fluid design. The second technology used to limit the height of the fracture was based on creating artificial barriers inside the fracture that restrict height growth. In this case, a special mixture of proppants was pumped before the primary proppant-laden fracturing main stage. The construction of a horizontal well with a multizone completion implies the possibility of carrying out small volume multistage fracturing to prevent breakthrough into a water-saturated interval, creating an effective drainage zone. For the first time in the given field, MS-Frac was performed using combined technologies and techniques for fracture height growth restriction. The operations demonstrated successful results of horizontal multizone well treatments, where the rheology and fluid rate control methods were used to restrict the fracture geometry growth, and proppant slugs were used to create artificial barriers to arrest the fracture height growth.
The Development of Chemical Stimulation Method Trends in Sandstone Reservoirs
Authors: Shcherbakov Georgii , Yakovlev Andrey , Groman Andrey , Maltcev Andrei
Published: October 2019

The article describes the main ideas of the integrated approach to the use of matrix-stimulation methods in the oilfields with sandstone reservoirs. LLC Gazpromneft scientific and technology center as the basis of the project "Optimal matrix stimulation methods" undertook the joint study. The main tasks of the project are related to the development of software tools such as: the tool for diagnosis of formation damage type in near-wellbore zone, the tool for selecting the optimal technology of near-wellbore treatment, the tool for matrix stimulation design with the possibility of it’s optimization.
The Opportunity of Drilled Solids Use in Lost Circulation Control
Authors: Salmina Tatiana , Shabzova Svetlana , Koval Maxim , Bogatkin Sergey
Published: October 2019

The design work contains development of the technology of circulation loss control during oil and gas wells drilling. Circulation loss control experience suggests that one of effective loss control methods is loss profiles plugging using inwash of fillers (shredded cellophane, cordage fiber, laminar elastic filler, etc.) In order to exclude the use of artificial fillers, it is proposed to use the drilled rock extracted from this well as a filler at the well drilling sites The special feature of the work is the use of travelling unit, which is installed on general platform and includes all required equipment to provide drilled cuttings injection into a well: slurry preparation block (screen shaker, breaking machine, mixing vessel, slurry storage tank) and slurry injection block (piston pump).  Before reinjection drilled solids are treated to the parameters, which can provide proper plugging of circulation loss channels (size and shape, chemical inactivity). The approach can decrease the volume of waste production during well construction process, exclude the use of artificial fillers and provide circulation loss control, which would lead to the decrease of ecological load. The applicability, advantages and disadvantages of the technology have been considered, risks analysis has been implemented and the opportunity of drilled solids use in circulation loss control has been thoroughly esteemed in terms of ecology and legislation as an example of AO Samaraneftegaz, the subsidiary of Rosneft.

Low formation pressure, water content, HFT high volumes, sufficient drainage volumes of Rosneft subsidiaries reservoirs – all the above leads to high risks of mud circulation loss during well drilling.

Annual circulation loss control time in oil and gas industry is equal to hundreds of thousands hours. Oil and gas wells construction consumes hundreds of thousands tons of casing strings and cement, millions m3 of drilling mud and chemicals.
Numerical Simulation of Hydrocarbon Mixtures Mass Transfer Processes and Flow in a Reservoir Rock
Authors: Grushnikov Ilya
Published: October 2019

Currently, a number of software products (PVTSim, WinProp CMG, Aspen HYSYS, etc.) are used in the oil and gas industry, simulating the interfacial mass exchange in natural oils, gas condensate mixtures, etc. Existing software products use the vapor-liquid equilibrium calculation methods (flash-calculations) based on various cubic equations of state for the hydrocarbon mixtures. Peng–Robinson and Soave–Redlich–Kwong equations of state are primarily used in these products. Within work (1), the author of current work created a software package in the Python language that can carry out vapor-liquid equilibrium numerical simulations for hydrocarbon mixtures (the paraffin series was considered) using three different cubic equations of state: Peng–Robinson, Soave–Redlich–Kwong and Brusilovskiy. The development of this software package allowed comparison the vapor-liquid equilibrium parameters for hydrocarbon mixtures calculated using these three equations of state.

The vapor-liquid equilibrium calculation for multicomponent hydrocarbon systems is also carried out in the numerical simulation of physicochemical processes in hydrocarbon deposits (simulators Eclipse 300, CMG GEM, etc.). Such calculations are important when the project to develop hydrocarbon deposits involves the injection of multicomponent gas mixtures ("fat" gas, air, etc.) in order to increase oil recovery. Here, using the created software package, we discuss how each of the three equations of state impact numerical simulation results of mass transfer processes between liquid and gas phases under fixed thermobaric conditions. The calculations help analyze how the choice of equation impacts simulation's results when extracting hydrocarbons.

The result of this work was the development of a software package for calculating the PVT parameters for multicomponent hydrocarbon systems in a compositional model based on the cubic equation of state (Peng–Robinson and Soave–Redlich–Kwong). The thermodynamic characteristics, such as density, viscosity and phase component composition, were calculated based on setting the total component composition, equation of state, pressure and temperature. After that, the results of the developed software package were compared with the results obtained using the popular software products for calculating the PVT properties for multicomponent hydrocarbon systems.
Improvement of Effectiveness of Hydraulic Fracturing in Carbonate Sediments P1ar+k of the Pashninskoe Field of the Komi Republic
Authors: Rakitin Evgeniy , Ziganshin Renat , Novokreshchennykh Dmitriy
Published: October 2019

The article describes the problem of low efficiency of acid and proppant hydraulic fracturing (HFT) using standard technology in conditions of closely spaced bottom waters of the low-permeable carbonate reservoir P1ar+k of the Pashninskoe field. The hydraulic fracturing technology has been optimized taking into account the geological and physical characteristics (GPC) of the reservoir under consideration and the main complicating factors in the implementation of well interventions (WI) for enhanced oil recovery (EOR). Optimized hydraulic fracturing technology showed high efficiency during testing. Well operation was monitored, according to the results of which the technology was transferred to the industrial category. The results of its replication are also presented. The average specific incremental oil rate from hydraulic fracturing according to the optimized technology was 0.68 tons/day/m, the oil production rate in 2018 increased by 9.4%.
Impact of toothpaste on oral health-related quality of life in people with dentine hypersensitivity
Authors: Mason Stephen , Burnett Gary R. , Patel Nisha , Patil Avinash , Maclure Robert
Published: October 2019

Abstract
Background: Dentine hypersensitivity can impact functional status and everyday activities such as eating and talking. This study aimed to assess changes in oral health-related quality of life measures in individuals with dentine hypersensitivity following long-term use (24 weeks) of a commercially available toothpaste marketed for dentine hypersensitivity relief.
Methods: This study was conducted across two sites and enrolled 75 adults with ≥2 non-adjacent sensitive teeth. Participants were assigned to twice-daily brushing with toothpaste containing 0.454% w/w stannous fluoride (1100 ppm fluoride). Every 4 weeks, participant-reported outcomes were assessed using the Dentine Hypersensitivity Experience Questionnaire (DHEQ), a condition specific oral health-related quality of life scale that has five domains and includes questions on social and emotional impact, restrictions, adaptations and effect on life overall. Responses to a clinically applied evaporative (air) stimulus were assessed using the examiner-observed Schiff sensitivity scale and Labelled Magnitude Scales (LMS), which included dentine hypersensitivity-specific descriptors of intensity, duration, tolerability and descriptive qualities of the participant’s response.
Results: Participant-reported outcomes demonstrated reduction of the impact of dentine hypersensitivity over time on health-related quality of life, as measured by the DHEQ. This reached statistical significance from Week 8 onwards (p<0.0001 versus baseline) for the Total DHEQ score, with scores continually decreasing at each timepoint. Most domain scores followed a similar pattern. Statistically significant reductions were also detected for the examiner-observed Schiff Sensitivity Scale scores at all timepoints (including at 4 weeks) (p<0.05), which were mirrored by LMS responses. The toothpaste was generally well-tolerated.
Conclusions: These results show that long-term use of a sensitivity toothpaste containing 0.454% w/w stannous fluoride has a beneficial, ongoing, impact on the oral health-related quality of life of people with dentine hypersensitivity.
Assessment of weight and height of patients with primary immunodeficiency disorders and group of children with recurrent respiratory tract infections.
Authors: Pieniawska-Śmiech Karolina , Bar Kamil , Babicki Mateusz , Śmiech Karol , Lewandowicz-Uszyńska Aleksandra
Published: October 2019

Background Primary immunodeficiences (PIDs) are a group of chronic, serious disorders in which the immune response is insufficient. In consequence, it leads to an increased susceptibility to infections. Up to date, there are about 300 different disorders classified in that group. There are also patients suffering from recurrent respiratory tract infections (RRTI), however that group doesn't present any abnormalities in terms of conducted immunological tests. Many factors, including medical, can have an impact on physical development of a child. Data such as birth weight and length, also weight, height, BMI during admission to the hospital were collected from 207 patients' medical histories from their hospitalization at Clinical Immunology and Paediatrics ward of J.Gromkowski Hospital in Wrocław. Investigated groups included patients with PIDs, RRTI and a control group of healthy children. Our purpose was to evaluate the physical growth of children with PID and children with RRTI by assessment of their height and weight. All of parameters were evaluated using centile charts suitable best for the Polish population. Results The lowest mean birth weight and height was found among the PIDs patients group. Children with PIDs during hospitalization had statistically relevant lower mean weight than the control group and almost 20% of them had their height situated below 3rd percentile. No statistically relevant differences have been found between them and RRTI group. The statistically significant difference was between the nutritional status of PID patients and the control group. Conclusions There is a higher percentage of PID patients with physical growth abnormalities in comparison to healthy children. Our findings indicate a need for further investigation of immune system irregularities and their influence on physical growth of children.
Use of patients’ unsolicited correspondence to a family doctor to describe and understand valued components of a doctor-patient relationship: A Hermeneutics approach
Authors: Yaffe Mark J. , Hovey Richard B. , Rodriguez Charo
Published: October 2019

Background Communication and behavior within doctor - patient encounters have been examined using varied techniques; however the nature of unsolicited writings from patients to their family doctors has rarely been reported. This paper therefore aimed to explore the content of, and motivation for, such correspondence. Methods 107 writings to one family physician about care provided during a four decade period were considered. Univariate analyses were used to identify features of patients or family members who wrote personalized notes to the doctor, when, and in what fashion. A hermeneutic approach helped look at the content of the notes, the specific words or sentiments used to describe encounters or care received, and possible motivations for writing. Iterative review of words or phrases generated themes which summarized appreciated physician or relational attributes, as well as motivations for writing. Results Notes were mostly handwritten, predominantly by women, and frequently coinciding with holidays and life span events. Appreciated doctor characteristics and behaviors were (1) quality care; and physician (2) competence; (3) physical presence; (4) positive personal traits; (5) provision of emotional support; and (6) spiritual impact. Motivations for writing were grouped as desire to (1) express appreciation for an established relationship; (2) acknowledge value / benefit experienced from continuity of care; (3) seek catharsis, emotional relief or closure; (4) reflect on termination of care; (5) validate care that incorporates both Hippocratic tradition and Asklepian healing ; and (6) share personal reflection, experience, or impact. Conclusions Unsolicited writings provide personalized links from patients to physicians, expressing thoughts perhaps difficult to share face to face. They offer potential as teaching tools about the content of doctor-patient relationships; for example, the writers studied expressed appreciation for quality continuity care that was competent, considerate, and supportive of emotional and spiritual needs.
Determinants Of Neonatal Mortality In The Largest International Border Of Brazil: A Case-Control Study
Authors: de Souza Suzana , Duim Etienne Larissa , Nampo Fernando Kenji
Published: October 2019

BACKGROUND: Foz do Iguassu is a Brazilian municipality located in the most populous international border of the country and provides medical care to foreigners. Neonatal mortality in the city is higher than Brazil’s average and corresponds to 61% of all deaths in children under five. The current study aimed to identify the determinants of neonatal mortality in Foz do Iguassu. METHODS: In this case-control study, we analyzed all neonatal deaths occurred in Foz do Iguassu from 2012 to 2016. Birth and mortality data were extracted from two national governmental databases (SINASC and SIM). We extracted data on (i) maternal sociodemographic characteristics, (ii) pregnancy care, and (iii) newborn characteristics. Multiple logistic regression with the conceptual framework was applied to examine the factors associated with neonatal mortality. RESULTS : Most of the deaths occurred in the early neonatal period (65.9%). The factors associated with neonatal death were fetal congenital anomaly (OR 22.49; CI 95% 7.44-67.95; p = <0.001); low birth weight (OR 17.15; CI 95% 8.56-34.37; p = <0.001), first minute Apgar score under 7 (OR 15.60; CI 95% 8.23- 29.67; p = <0.001); zero to 3 prenatal appointments (OR 3.34; CI 95% 1.28-8.73; p = 0.014) and prematurity (OR 3.60; CI 95% 1.87‑7.11; p = <0.001). CONCLUSION : The high rate of neonatal death in Foz do Iguassu is strongly associated with newborn characteristics and not associated with maternal sociodemographic characteristics. Thus, the health services in the Brazilian side of this international borders should be aware of the quality of the prenatal care and childbirth attention provided.
Risk factors for peritonitis in patients on continuous ambulatory peritoneal dialysis who undergo colonoscopy: A retrospective multicentre study
Authors: Gweon Tae-Geun , Jung Sung Hoon , Kim Sang Woo , Lee Kang-Moon , Cheung Dae Young , Lee Bo-In , Choi Hwang
Published: October 2019

Background: Colonoscopy is associated with a risk of peritonitis in patients on peritoneal dialysis. However, no study has yet described the risk factors in play. Methods: This was a retrospective multicentre study. The medical records of patients on continuous ambulatory peritoneal dialysis (CAPD) who underwent colonoscopy from January 2003 to December 2012 were analysed. We recorded demographic characteristics, colonoscopic factors, use of prophylactic antibiotics, and development of peritonitis. Colonoscopy-related peritonitis was defined as peritonitis developing within 1 week after colonoscopy. Demographic and clinical characteristics were compared between patients who did and those who did not develop peritonitis. Results: During the study period, 236 patients on CAPD underwent colonoscopy, of whom 9 (3.8%) developed peritonitis. The rates of polypectomy/endoscopic mucosal resection were significantly higher in the peritonitis group than in the no peritonitis group (66.7 vs. 23.4%, p=0.009). Prophylactic antibiotics were prescribed before colonoscopy in 65 patients; none developed peritonitis. No patient who developed peritonitis received prophylactic antibiotics (p=0.067). Conclusions: Advanced procedures including polypectomy or endoscopic mucosal resection increase colonoscopy-related peritonitis in patients on CAPD. Randomized controlled trials to investigate whether prophylactic antibiotics are needed to prevent peritonitis in all CAPD patients are warranted.
Prevalence of geriatric depression in the Kavre district, Nepal: Findings from a cross sectional community survey
Authors: Manandhar Kedar , Risal Ajay , Shrestha Oshin , Manandhar Nirmala , Kunwar Dipak , Koju Rajendra , Holen Are
Published: October 2019

Abstract

Background: The increasing elderly population worldwide is likely to increase mental health problems such as geriatric depression, which has mostly been studied in high-income countries. Similar studies are scarce in low-and-middle-income-countries like Nepal.

Methods: A cross-sectional, population-based, door-to-door survey was conducted in randomly selected rural and urban population clusters of the Kavre district, Nepal. Trained nurses (field interviewers) administered structured questionnaires that included a validated Nepali version of the Geriatric Depression Scale short form (GDS-15) for identifying geriatric depression among the elderly (≥60 years) participants (N=460). Those scoring ≥6 on GDS-15 were considered depressed. Logistic regression analysis explored the associations of geriatric depression with regard to socio-demographic information, life style, family support and physical well-being.

Results: Of the total 460 selected elderly participants, 439 (95.4%) took part in the study. More than half of them were females (54.2%). The mean age was 70.9 (± 8.6) years. Approximately half (50.6%) were rural inhabitants, the majority (86.1%) were illiterate, and about three-fifths (60.1%) were living with their spouses. The gender-and-age adjusted prevalence of geriatric depression was 53.1%. Geriatric depression was significantly associated with rural habitation (AOR 1.6), illiteracy (AOR 2.1), limited time provided by families (AOR 1.8), and exposure to verbal and/or physical abuse (AOR 2.6).

Conclusion: Geriatric depression is highly prevalent in Kavre, Nepal. The findings call for urgent prioritization of delivery of elderly mental health care services in the country.

Keywords: depression, elderly, lifestyle, mental health, prevalence
Sociodemographic characteristics associated with alcohol consumption and alcohol-related consequences, a latent class analysis. The Norwegian WIRUS screening study.
Authors: Skogen Jens Christoffer , Bøe Tormod , Thørrisen Mikkel Magnus , Riper Heleen , Aas Randi Wågø
Published: October 2019

Background: For alcohol, the association with socioeconomic status (SES) is different than for other public health challenges – the associations are complex, and heterogeneous between socioeconomic groups. Specifically, the relationship between alcohol consumption per se and adverse health consequences seems to vary across SES. This observation is called the ‘alcohol harm paradox’. This study aims to describe different patterns of alcohol use and potential problems. Next, the associations between sub-groups characterized by different patterns of alcohol use and potential problems, and age, gender, educational level, full-time employment, occupational level and income is analysed.
Methods: Employing data from the ongoing cross-sectional WIRUS-study, N=4,311 participants were included in the present study. Individual response patterns of the ten-item Alcohol Use Disorders Identification Test (AUDIT) were analysed and latent class analysis (LCA) was used to identify latent groups. Next, the associations between the classes identified in the best fitting LCA-model and sociodemographic factors were analysed and presented.
Results: We identified three classes based on the response patterns on AUDIT. Class 1 was characterised by low-level alcohol consumption and very low probability of negative alcohol-related consequences related to their alcohol consumption. Class 2 was characterised by a higher level of consumption, but despite this, class 2 also had a relatively low probability of reporting negative alcohol-related consequences. Class 3, however, was characterised by high levels of alcohol consumption, and a high probability of reporting negative consequences of their consumption. The classes identified were systematically differentially associated with the included measures of SES, with class 3 characterised by younger age, more males and lower educational attainment.
Conclusions: Our findings highlight the interconnectedness of alcohol consumption and alcohol-related consequences. Further, our related the identified classes and SES yields further insights into to intricate relationship between various socioeconomic factors, alcohol use patterns and related negative consequences.
Rice of Northeast India harbor rich genetic diversity as measured by SSR markers and Zn/Fe content
Authors: Surname Vanlalsanga No , Singh Sagolshem Priyokumar , Singh Yengkhom Tunginba
Published: October 2019

Background Rice (Oryza sativa L.) is one of the most important crops of the world and a major staple food for half of the World’s human population. The Northeastern (NE) region of India lies in the Indo-Burma biodiversity hotspot and about 45% of the total flora of the country is found in the region. Local rice cultivars from different states of NE India were analyzed for genetic diversity and population structure using microsatellite markers, and their zinc and iron content. Results A total of 149 bands were detected using twenty-two microsatellite markers comprising both random and trait-linked markers, showing 100% polymorphism and high value of expected heterozygosity (0.6311) and the polymorphism information content (0.5895). Nali Dhan cultivar of Arunachal Pradesh possessed the highest genetic diversity (0.3545) among studied populations while Moirangphou Khonganbi of Manipur exhibited the lowest genetic diversity (0.0343). The model-based population structure revealed that all the studied 65 rice cultivars were grouped into two clusters. Cluster I was represented by 36 cultivars and cluster II by 29 cultivars. Badalsali cultivar of Assam possessed the highest Zn content (75.8 μg/g) and Kapongla from Manipur possessed the lowest (17.98 μg/g). The highest and the lowest Fe content was found in Fazu (215.62 μg/g) and Idaw (11.42 μg/g) of Mizoram. Conclusion The result suggested rice cultivars of NE India possessing high genetic diversity (Nali Dhan), high Zn (Badalsali) and Fe (Fazu) content can be useful as a source of germplasm for future rice improvement programs.
Persistent domestic circulation of African swine fever virus in Tanzania, 2010-2017
Authors: Yona Clara M. , Vanhee Merijn , Simulundu Edgar , Makange Mariam , Nauwynck Hans , Misinzo Gerald
Published: October 2019

Background African swine fever (ASF) is a highly fatal viral hemorrhagic disease of domestic pigs that threatens livelihoods and food security. In Africa, ASF virus (ASFV) circulates in sylvatic (transmission between warthogs and soft argasid ticks) and domestic (transmission between domestic pigs) cycles, with outbreaks resulting from viral spill-over from sylvatic cycle. The present study investigated ASFV transmission patterns through virus genotyping. Results Genotypes II, IX, X, XV and XVI of ASFV were found to circulate and maintained by transmission between domestic pigs. Methods In addition to archived samples, tissue samples were collected from domestic pigs during outbreaks at different locations in Tanzania between 2015 and 2017 followed by nucleotide sequencing and phylogenetic analysis of B646L gene of ASFV. Conclusion Maintenance of ASFV in the domestic cycle was due to bleach of quarantine and transportation of affected pigs via major highways. Appropriate control measures including sanitary measures at the slaugher slabs and quarantine measures adherence are recommended to prevent ASF emergence and re-emergence in Tanzania. Transportation of pig and pig products for regional market should be controlled to prevent ASFV spreading to other states of the East African Community , as ASFV genotype II has spread beyond its geographical range.
Trajectory of serum uric acid as a predictor for renal outcome and mortality in stage -3 chronic kidney disease patients
Authors: Tsai Shangfeng , Chen Cheng-Hsu , Wu Ming-Ju , Lee Chia-Lin
Published: October 2019

IntroductionUric acid (UA) is associate with renal and patient survival but the association is causal in nature remains unclear. Also, no finding is yet available regarding longitudinal UA control (trajectory). Methods We enrolled 808 subjects diagnosed with stage 3 CKD from 2007 to 2017. We plotted based on follow-ups the mean UA over a period of 6 months with a minimum of three samples of UA was required. From the sampled points, we generated for each patient an interpolated line by joining mean values of the UA levels over time. And from the lines from all patients, we classified them into three groups of trajectories (low, medium and high UA) through group-based trajectory modeling, and then further separated into either a treatment or no-treatment subgroups. Using the univariate competing-risks regression, we calculated the competing risk analysis with subdistribution hazard ratio of possible confounders.Results All of the 6 trajectories appeared as gradually falling functions with time without any of the curves crossed over one another. For all-cause mortality risk, none of the variables was statistically significant. Patients with DM were statistically more likely to undergo dialysis. There was also a trend that the on-treatment trajectories, compared to their no-treatment trajectories, had lower risks for dialysis.Conclusions Initial treatment of UA is utterly important. Xanthine oxidase inhibitors may lead to renal protection without effects on patient death, independent from the UA-lowering effects. This is the first study on the long-term effects of UA trajectory on patient survivals and renal outcomes.
Bioinformatic prospecting identified 99 novel, misannotated and unnoticed putative circular bacteriocins
Authors: Vezina Ben , Rehm Bernd H.A. , Smith Andrew T.
Published: October 2019

Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are nineteen experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence. Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 118. They were grouped into two families within class IIc (IIc i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes. Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.
Determinants of application of the multilevel approach in management of a non-communicable disease in Denmark
Authors: Noor Fadumo Abdi , Søndergaard Jens , Gulis Gabriel
Published: October 2019

Background Working at multiple levels (intrapersonal, interpersonal and structural) and within multiple settings (medical, communities/municipalities, regional, and governmental) plays a significant role in promoting health and preventing chronic diseases. We analyzed determinants of the use of multilevel approach-based work on the example of the management of type II diabetes in the Region of Southern Denmark.Method A qualitative interview study comprising 19 individual interviews with health professionals at different levels and two focus group interviews with diabetes patients in municipalities of the Region of Southern Denmark.Results Communication, funding, lack of clarity of content and aims of collaboration, and organizational, structural, and legislative issues were identified as the main barriers to effective multilevel approach-based management of type II diabetes.Conclusion Organizational, structural and capacity-related barriers should be addressed in order to develop an effective multilevel public health approach to target type II diabetes and potentially other non-communicable diseases.
Open Partial Nephrectomy without Ischemia
Authors: rabani seyed mohammadreza , Mousavizadeh Ali , rabani seyedhossein
Published: October 2019

Background: Vascular clamping during partial nephrectomy could induce to renal ischemia and kidney’s damage due to reperfusion injuries. Adverse effect on renal function can be eliminated by Zero ischemia techniques.The aim of this study was to assess the feasibility of performing partial nephrectomy under a situation of being ready to clamping renal artery.
Methods: 24 patients with solitary small renal masses were recruited to the study between 2013and 2018. Open partial nephrectomy was performed for them. During the time corresponding to hilar vessels clamping in standard procedures, we have reached to the renal artery and ready for clamping if needed, and in this situation resection of the mass was assessed.
Results The mean age of patients was 42 years. The tumor resection time was 22 minutes averagely. The median procedure time was 92 minutes, Clear cell RCC was found in 19 patients, papillary RCC in 3 and oncocytoma in 2 with no positive surgical cancerous margin in specimens. Lower pole, midzone and upper pole masses were found consequently in14, 2 and 8 cases.
Conclusions: Although this technique could be a dangerous decision making in a well exposed renal artery, especially in Polar Regions, the tumor resection can be safely conducted without ischemia.
Management of stretched scar– induced secondary strabismus
Authors: Farid Mohamed F , Awwad Mohamed A , Mahmoud Mohamed R
Published: October 2019

BACKGROUND: To determine characteristics and management of consecutive or recurrent strabismus secondary to stretched scar. METHODS: This is a retrospective review of all patients diagnosed with late secondary consecutive or recurrent strabismus due to stretched scar from 2012 to 2017. The diagnosis of stretched scar was made in any case of late (≥ 1 month) consecutive or recurrent strabismus associated with underaction of the previously operated muscle. The diagnosis was confirmed intraoperatively by negative forced duction test and the characteristic appearance of the scar tissue. Surgical correction involved excision of the scar tissue with muscle re-attachment to the sclera using non-absorbable sutures. Study parameters include improvement in secondary deviations, degree of muscle underaction and diplopia. RESULTS: 21 consecutive and 6 recurrent cases of stretched scar –induced strabismus were identified and all cases were associated with variable degrees of limited ocular duction. After surgical correction of the stretched scar, consecutive deviations in the form of consecutive esotropia and exotropia were corrected by means of 26.1PD and 65.6PD while recurrent deviations in the form recurrent exotropia and recurrent hypertropia were corrected by means of 34.3PD and 11PD respectively with significant improvement of limited ocular ductions. 21 patients had diplopia at presentation and all were improved after surgery. CONCLUSION: management of stretched scar –induced secondary strabismus by excision of the stretched scar and muscle fixation to the sclera using non-absorbable sutures significantly corrects secondary deviations and improves limitation of ocular duction.
Protein Remote Homology Detection Based on Deep Convolutional Neural Network
Authors: Wang Yu , Bao JunPeng , Huang Fangfang , Du Jianqiang , Li Yongfeng
Published: October 2019

Background: Protein remote homology detection has long received great attention in the field of bioinformatics, but the property of low protein sequence similarities heavily influences the accuracy of detection. Recently, such deep learning methods as LSTM have been adopted to deal with the problem. However, LSTM-based models will consume much time during the training process because of their cyclic connection mechanism and such problem will become more serious when dealing with long protein sequences. Results: In this paper, we propose a CNN-based network, called ConvRes, to address the aforementioned shortcomings of existing methods in this field, which combines a variant Inception and Resnet block. Experimental results show that (1) this CNN-based network can classify the family of the remote homology proteins with comparable precision to the existing state-of-art method (ProDec-BLSTM) on the SCOP benchmark dataset. (2) ConvRes consumes less time with using only 15000 seconds whereas ProDec-BLSTM taking 150000 seconds. Conclusion: This paper showcases that our proposed ConvRes network outperforms other existing models with regard to detecting remote homology proteins. The experimental results prove ConvRes network to be a viable and efficient model for remote homology protein detection. In the future work, we will improve the performance of ConvRes network by using other dataset and explore new representations to adapt for variable-length sequences.
Clinical pictures, treatments, resource use, and costs of norovirus gastroenteritis in long-term care facilities: A survey with a chart review in Japan
Authors: Fujiki Saori , Ishizaki Tatsuro , Nakayama Takeo
Published: October 2019

Background

Outbreaks of norovirus infection can have detrimental impacts on long-term care facilities. This study investigated the incidence, clinical picture, treatment, resource use, and costs of norovirus gastroenteritis in long-term care facilities.

Methods

Nineteen facilities in Osaka and Kyoto, Japan participated in questionnaire surveys conducted between 2009 and 2011 regarding the incidence of norovirus gastroenteritis. From clinical charts, the characteristics, symptoms, and treatment of infected residents were analyzed. Total drug cost per infected resident was calculated by multiplying the unit price for each drug by the daily dose and the number of days administered and summing the costs for each drug (USD 1 = JPY 100).

Results

Over the 3-year period, 8 outbreaks of norovirus gastroenteritis occurred in 6 facilities. The mean clinical course of 107 infected residents in five facilities that granted permission to examine patients’ medical records was 4 days, with all but one resident presenting with vomiting and/or diarrhea, and 84 (79%) also presenting with associated symptoms. Of 107 infected residents, 72 (67%) were isolated. The proportion of infected residents isolated varied from 50% to 100% depending on the facility. Of the infected residents, 81 (76%) received some type of medication, the most common being infusion (67 patients, 63%) and antibiotics (30 patients, 28%). The median total cost of all drugs administered was USD 4.4, and the median drug cost per infected resident per day was USD 2.0. Total drug cost over the entire treatment period was the highest for antibiotics, at USD 8.6.

Conclusion

Clinical course was similar to those of norovirus cases examined at other facilities. The majority of infected residents received some type of medication. Although the economic burden was not large, not a few infected residents were given antibiotics, which are ineffective for norovirus.
Potential and realised endozoochorous dispersal by herbivores and omnivores in a Caspian forest steppe area
Authors: Karimi Sorour , Hemami Mahmoud-Reza , Esfahani Mostafa Tarkesh , Baltzinge Christophe
Published: October 2019

Background: Among other factors, feeding regimes of different mammals affect their roles as endozoochorous seed dispersal vectors. We thus conducted a cross-species comparative approach involving two herbivores, red and roe deer; and two omnivores and opportunistic frugivores, wild boar and brown bear, which occupy the forest and prairie-forest ecotone habitats of the south-eastern Caspian region. To compare their potential and realised endozoochorous seed dispersal, we used two different seed germination methods: controlled greenhouse and natural conditions.
Results: Of the 136 plant taxa (3078 seedlings) recorded from the 445 paired dung sub-samples of both methods, only 36 taxa (336 seedlings) were recorded under natural conditions, among which five taxa showed no emergence in the greenhouse. Graminoids and forbs composed 91% of the seedlings in greenhouse but shrub species were more abundant under natural conditions (55% of emerged seedlings). Considering greenhouse condition, red deer and then wild boar dispersed more species than the other animals, while in natural condition brown bear was the most effective vector. We observed remarkably higher species richness and seedling abundance in the controlled greenhouse method than natural condition (P≤0.001). This difference may be related to dung sample preparation method or meteorological conditions in the field during our experiment.
Conclusions: The studied sympatric vectors were shown to provide different seed dispersal services and may, therefore, be regarded as complementary. Our results provide evidence for the potential positive bias arising when only considering germination under controlled greenhouse conditions. Relativising the potential versus the realised endozoochorous dispersal of seeds by different mammals would help determine management options to maintain plant biodiversity.
Keywords : Different germination methods, Mammal functional groups, Potential endozoochory, Realised endozoochory
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties
Authors: Khatri Indu , Sharma Gaurav , Subramanian Srikrishna
Published: October 2019

Background: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.
Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina ® and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor higher heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens S. aureus and S. epidermidis , were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in Bacillus clausii and other probiotics.
Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains and industrially relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections.
Explaining the successes and failures of tuberculosis treatment programs; a tale of two regions in rural Eastern Uganda
Authors: Izudi Jonathan , Tamwesigire Imelda K , Bajunirwe Francis
Published: October 2019

Background Well performing tuberculosis (TB) programs are characterized by treatment success rate (TSR) of at least 90%. In rural eastern Uganda, and elsewhere in sub Saharan Africa, TSR varies considerably across district TB programs and the reasons for the differences are unclear. This study explored factors that explain the low and high TSR across four districts in rural eastern Uganda.Methods We interviewed District TB and Leprosy Supervisors (DTLS), Laboratory focal persons (LFPs) and TB focal persons (TBFPs) from four districts in Eastern Uganda as key informants. Interviews were audio recorded, transcribed verbatim, and imported into ATLAs.ti where thematic content analysis was performed and results were summarized into themes.Results The emerging themes were categorized as either facilitators of or barriers to treatment success. The emerging facilitators prevailing in the districts with high rates of treatment success were using data to make decisions and design interventions, continuous quality improvement, capacity building, and considered TB as a priority disease. The barriers that were common in districts with low rates of treatment success included lack of motivated and dedicated TB focal persons, scarce or no funding for implementing TB activities, and a poor implementation of community-based directly observed therapy short course.Conclusion This study shows several factors account for the differing rates of treatment success in rural eastern Uganda. These factors should be the focus for TB control programs in Uganda and similar settings in order to improve rates of treatment success.