bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Analysis of Computed Tomography and Laparoscopy Data in Preoperative Staging of Gastric Cancer
Authors: Silanteva N. K. , Аgababyan T. A. , Kholeva A. A. , Skoropad V. Yu. , Shavladze Z. N. , Ivanov S. A. , Zhavoronkov L. P. 
Published: January 2021

Objective: to compare the data of computed tomography (CT) and diagnostic laparoscopy (DL) in the preoperative estimation of the extension of gastric cancer.Material and methods. Data on 51 patients with a histologically confirmed diagnosis of gastric cancer were analyzed. CT and DL were performed in all the patients at an interval of 1–2 days during their preoperative examinations to determine the stage of a tumor process. Of the 51 patients, 34 (66.7%) were found to have no distant abdominal metastases and underwent radical surgery. CT and DL revealed distant abdominal organ metastases in 17 (33.3%) of the 51 patients. To evaluate the diagnostic efficiency of CT and DL, the investigators calculated the main characteristics (sensitivity, specificity) and auxiliary criteria (accuracy, positive (PPV) and negative (NPV) predictive values.Results. The findings suggested that the diagnostic efficiency of CT in determining the T category was a sensitivity of 86% and a specificity of 92%; and that of DL was 83% and 87%, respectively. CT in diagnosing a regional lymph node metastasis had a higher sensitivity than DL (88% vs. 63%), but a lower specificity than DL (80% vs. 90%). CT diagnosis of peritoneal carcinomatosis exhibited a sensitivity of 46%, a specificity of 97.4%, an accuracy of 84.3%, PPV of 85.7%, and NPV of 84.1%. The symptoms of peritoneal carcinomatosis were ascites, soft tissue nodules along the peritoneum, diffuse induration and thickening of abdominal tissue planes, and increased mesenteric vascularity.Conclusion. The combined use of CT and DL is a current algorithm for examining patients with gastric cancer. It makes it possible to obtain complete information about the extension of the process, to increase the accuracy of preoperative diagnosis and to form a group of patients to undergo radical surgery.
Partial Distal Biceps Avulsion Results in a Significant Loss of Supination Force
Authors: Tomizuka Yoshiaki , Schmidt Christopher C. , Davidson Anthony J. , Spicer Christopher S. , Smolinski Michael P. , Mauro Ryan J. , Delserro Sean M. , Szabo Linsey H. , Smolinski Patrick J. , Miller Mark Carl 
Published: January 2021

Background:
Partial avulsions of the short and/or long head of the distal biceps tendon cause pain and loss of strength. The goal of the present study was to quantify the loss of supination and flexion strength following a series of surgical releases designed to simulate partial and complete short and long head traumatic avulsions.

Methods:
Mechanical testing was performed to measure supination moment arms and flexion force efficiency on 18 adult fresh-frozen specimens in pronation, neutral, and supination. The distal biceps footprint length was divided into 4 equal segments. In 9 specimens (the distal-first group), the tendon was partially cut starting distally by releasing 25%, 50%, and 75% of the insertion site. In the other 9 specimens (the proximal-first group), the releases started proximally. Mechanical testing was performed before and after each release.

Results:
Significant decreases in the supination moment arm occurred after a 75% release in the distal-first release group; the decrease was 24% in pronation (p = 0.003) and 10% in neutral (p = 0.043). No significant differences in the supination moment arm (p ≥ 0.079) or in flexion force efficiency (p ≥ 0.058) occurred in the proximal-first group.

Conclusions:
A simulated complete short head avulsion significantly decreased the supination moment arm and therefore supination strength.

Clinical Relevance:
A mechanical case can be made for repair of partial distal biceps tendon avulsions when the rupture involves ≥75% of the distal insertion site.
Maternal Caffeine Consumption and Racial Disparities in Fetal Telomere Length
Authors: Griffin Isabel , Ibrahimou Boubakari , Navejar Natasha , Aggarwal Anjali , Myers Kristopher , Mauck Daniel , Yusuf Korede K. , Wudil Usman J. , Aliyu Muktar H. , Salihu Hamisu M. 
Published: January 2021

Background and Objectives: The identification of risk factors for shorter telomere length, especially during fetal development, would be important towards caffeine consumption recommendations for pregnant women on a global scale. The purpose of this study was to evaluate the association between caffeine intake and fetal telomere length as well as racial/ethnic differences in telomere length regardless of maternal caffeine consumption status.
Methods: Caffeine intake was measured using a food frequency questionnaire (FFQ). Three generalized linear models (GLM) were compared based on binary categorical variables of caffeine levels using data mean value of 117.3 mg as cut-off; the World Health Organization (WHO) recommendations of 300 mg; and the American College of Obstetricians and Gynecologists (ACOG) recommendations of 200 mg. The association between caffeine consumption and telomere length (telomere to single-copy [T/S] ratio) was then assessed.
Results: Among 57 maternal-fetal dyads, 77.2% reported less than 200 mg of caffeine (ACOG) and 89.5% less than 300 mg (WHO). Both WHO and ACOG models found that caffeine intake was significantly and positively associated with longer telomere length (p<0.05); and sodium (p<0.05). Other” race (p<0.001) and “white” race (p<0.001) were also significantly and positively associated with longer telomere length in the same models. Increasing maternal age shortened telomere length significantly in all models (p<0.001).
Conclusion and Global Health implications: Caffeine intake, maternal age, and race may be associated with alterations in fetal telomere length. This indicates that caffeine consumption during pregnancy may have long-term implications for fetal development. The racial/ethnic differences in telomere length found in this study warrant larger studies to further confirm these associations.
Key words: • Telomere • Fetal telomere length • Caffeine • Pregnancy • Maternal-Fetal medicine • Racial/ethnic differences

Copyright © 2020 Griffin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
Guest Editorial: Artificial Intelligence in the E&P Industry: What Have We Learned So Far and Where to Next?
Authors: Pathak Manas , Cosby Tonya , Perrons Robert K. 
Published: January 2021

Artificial intelligence (AI) has captivated the imagination of science-fiction movie audiences for many years and has been used in the upstream oil and gas industry for more than a decade (Mohaghegh 2005, 2011). But few industries evolve more quickly than those from Silicon Valley, and it accordingly follows that the technology has grown and changed considerably since this discussion began. The oil and gas industry, therefore, is at a point where it would be prudent to take stock of what has been achieved with AI in the sector, to provide a sober assessment of what has delivered value and what has not among the myriad implementations made so far, and to figure out how best to leverage this technology in the future in light of these learnings.
When one looks at the long arc of AI in the oil and gas industry, a few important truths emerge. First among these is the fact that not all AI is the same. There is a spectrum of technological sophistication. Hollywood and the media have always been fascinated by the idea of artificial superintelligence and general intelligence systems capable of mimicking the actions and behaviors of real people. Those kinds of systems would have the ability to learn, perceive, understand, and function in human-like ways (Joshi 2019). As alluring as these types of AI are, however, they bear little resemblance to what actually has been delivered to the upstream industry. Instead, we mostly have seen much less ambitious “narrow AI” applications that very capably handle a specific task, such as quickly digesting thousands of pages of historical reports (Kimbleton and Matson 2018), detecting potential failures in progressive cavity pumps (Jacobs 2018), predicting oil and gas exports (Windarto et al. 2017), offering improvements for reservoir models (Mohaghegh 2011), or estimating oil-recovery factors (Mahmoud et al. 2019).
But let’s face it: As impressive and commendable as these applications have been, they fall far short of the ambitious vision of highly autonomous systems that are capable of thinking about things outside of the narrow range of tasks explicitly handed to them. What is more, many of these narrow AI applications have tended to be modified versions of fairly generic solutions that were originally designed for other industries and that were then usefully extended to the oil and gas industry with a modest amount of tailoring. In other words, relatively little AI has been occurring in a way that had the oil and gas sector in mind from the outset.
The second important truth is that human judgment still matters. What some technology vendors have referred to as “augmented intelligence” (Kimbleton and Matson 2018), whereby AI supplements human judgment rather than sup-plants it, is not merely an alternative way of approaching AI; rather, it is coming into focus that this is probably the most sensible way forward for this technology.
Geocognitive Technologies Improve Basin- and Petroleum-System Analyses
Authors: Carpenter Chris 
Published: January 2021

This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper SPE 197610, “Application of Geocognitive Technologies to Basin- and Petroleum-System Analyses,” by Paolo Ruffo, Marco Piantanida, SPE, and Floriana Bergero, Eni, et al., prepared for the 2019 Abu Dhabi International Petroleum Exhibition and Conference, Abu Dhabi, 11-14 November. The paper has not been peer reviewed.
Eni and IBM developed a cognitive engine exploiting a deep-learning approach to scan documents searching for basin geology concepts, extracting information about petroleum system elements (e.g., formation name; geological age; and lithology of source rocks, reservoirs, and seals), and enabling basin geologists to perform automated queries to collect all information related to a basin of interest. The cognitive engine succeeded in identifying the correct formations, lithologies, and geological ages of the petroleum systems with an accuracy in the range of 75 to 90%.
Introduction
While commercial databases often provide summary information about basins that can be extracted easily with queries or even interactive tools, the explorationist needs to integrate such information with more up-to-date and in-depth descriptions of structural and sedimentary events occurring in the basin, descriptions that can be found only in unstructured documents. Key information about basins can be scattered across paragraphs, tables, and image captions of hundreds of technical articles, or can be embedded within pictures. Even when exploiting a traditional search engine with the name of the desired basin, the results can be unsatisfactory: first, not all the results might be relevant; second, many different variants of the basin name are often used within publications. In the optimistic hypothesis that the subset of relevant documents is found by the search engine, all key concepts related to a basin need to be understood by the geologist by careful examination of the paper text and images.
Moreover, even if the published information (structured and unstructured) on a basin is found, there are different opinions expressed by different authors, in addition to the uncertainty of the data itself (such as the age of a formation or the details of the geological evolution of the basin), so that multiple conceptual models of the basin can be drawn from the uncertain and scarce information available. Some of these conceptual models are more probable while others are less probable, but sometimes the latter happen to be economically more valuable. Therefore, recovery of all relevant information about a basin is crucial, but also important is the preservation of differing opinions about the data - what might be termed minority reports.
Digital Transformation Enables Automated Real-Time Torque-and-Drag Modeling
Authors: Carpenter Chris 
Published: January 2021

This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper SPE 199670, “Digital Transformation Strategy Enables Automated Real-Time Torque-and-Drag Modeling,” by Dingzhou Cao, Occidental Petroleum; Don Hender, SPE, IPCOS; and Sam Ariabod, Apex Systems, et al., prepared for the 2020 IADC/SPE International Drilling Conference, Galveston, Texas, 3-5 March. The paper has not been peer reviewed.
Automated real-time torque-and-drag (RT-T&D) analysis compares real-time measurements with evergreen models to monitor and manage downhole wellbore friction, improving drilling performance and safety. Enabling RT-T&D modeling with contextual well data, rig-state detection, and RT-interval event filters poses significant challenges. The complete paper presents a solution that integrates a physics-based T&D stiff/soft string model with a real-time drilling (RTD) analytics system using a custom-built extract, transform, and load (ETL) translator and digital-transformation applications to automate the T&D modeling work flow.
Methodology
A T&D representational state transfer (REST) application program interface (API) was integrated with an RTD analytics system capable of receiving and processing both real-time (hookload, torque, and rig-state) and digitized (drillstring and casing components, trajectory profiles, and mud-property) well data across multiple platforms. This strategy consists of four parts:
Digital transformation apps, ETL, and translator
Physics-based stiff/soft string T&D model API
Pre-existing data infrastructure
RTD analytics system
The data-flow architecture reveals a flexible design in the sense that it can accommodate different types of T&D models or any other physics-based REST API models (e.g., drillstring buckling or drilling hydraulics) and can be accessed offline for prejob/post-job planning. Drilling engineers can also leverage the RTD systems’ historical database to perform recalculations, comparative analysis, and friction calibrations. The RT-T&D model also can be deployed in a cloud environment to ensure that horizontal scalability is achieved.
Analysis of Torsional Stick-Slip Situations from Recorded Downhole Rotational Speed Measurements
Authors: Cayeux E. , Ambrus A. , Øy L. , Helleland A. , Brundtland S. T. , Nevøy H. , Morys M. 
Published: January 2021

Summary
The use of recorded downhole rotational speed measurements with a bandwidth up to 9 Hz gives new insights into the conditions under which stick-slip torsional oscillations occur. Observations made while drilling two reservoir sections have shown that, out of all the stick-slip situations identified, 72% of them for one well and 64% for the other well occurred in off-bottom conditions. In these off-bottom conditions, stick-slip was systematically observed while starting the topdrive (TD) until a sufficiently high TD rotational velocity was requested. For these two sections, off-bottom stick-slip was either related to using TD speeds below 120 rev/min or to reaming down during reciprocation procedures. In on-bottom conditions, stick-slip events occurred predominantly when the TD speed was less than 120 rev/min (53 and 32% of the on-bottom cases) but also in association with downlinking to the rotary steerable system (RSS) (23 and 46% of the on-bottom cases), and this, even though the TD speed was larger than 120 rev/min. These on-bottom stick-slip situations did not necessarily occur at a very high weight on bit (WOB) because 98% of them for one well and 46% for the other well took place when the WOB was lower than 10 ton. Downhole measurements have shown that when the drillstring is subject to strong stick-slip conditions, the downhole rotational speed changes from stationary to more than 300 rev/min in just a fraction of a second. Direct observations of downhole rotational speed at high frequency help in discovering conditions that were not suspected to lead to large torsional oscillations. This new information can be used to improve drilling operational procedures and models of the drilling process, therefore enabling increased drilling efficiency.
Influence of 200 years of water resource management on a typical central European river Does industrialization straighten a river?
Authors: Wolf Stefanie Sabine , Esser Verena , Schüttrumpf Holger , Lehmkuhl Frank 
Published: January 2021

Abstract
Background Over the last 200 years, the courses of most European rivers have experienced significant irreversible changes. These changes are connected to different kinds of anthropogenic river use and exploitation, which have varied from running water mills and rafting to large-scale hydroelectric power plants, industrial water withdrawal and flood protection measures. Today, in most developed countries, water quality and ecological river development are important factors in water management. The aim of this study is to evaluate the specific impacts of different time periods during the last 200 years on river courses and their effects on current river management using the example of the 165 km-long German Rur River (North Rhine-Westphalia). The Rur River is a typical central European upland to lowland river whose catchment has been affected by various phases of industrial development.MethodsIn this study, a range of morphological changes over the last 200 years are determined based on historic maps and up-to-date orthophotos. River length, sinuosity, oxbow structures, sidearms and the number of islands are used to investigate human impact. The results are correlated with historic time periods.ResultsThis analysis shows that river straightening increases, especially during the Industrial Revolution, even without direct hydraulic channelization. The period and grade of river straightening have a direct morphodynamic impact on today’s river restorations. Since the Rur River is a typical upland to lowland river, the results show an additional impact by geofactors, such as landform configurations.ConclusionsMorphodynamic development is correlated with five historic periods of industrial development between 1801 and 2019 up to the introduction of the EU - Water Framework Directive (EU-WFD). Each period shows a different influence on the watercourse, which is connected with human intervention. Even if worldwide comparisons show that the five historical phases differ slightly in their timing between regions, they are applicable to other study areas.
Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China
Authors: Zhao Kuangjie , Yin Yueyan , Hua Mengying , Wang Shaoxiang , Mo Xiaohan , Yuan Enping , Zheng Hongying , Lin Lin , Chen Hairu , Lu Yuwen , Chen Jianping , Peng Jiejun , Yan Fei 
Published: January 2021

Abstract
Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5’ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3’-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126-5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.
Pilot Evaluation of an Enzymatic Assay for Rapid Measurement of Antiretroviral Drug Concentrations
Authors: Olanrewaju Ayokunle O. , Sullivan Benjamin P. , Bardon Ashley R. , Lo Tiffany J. , Cressey Tim R. , Posner Jonathan D. , Drain Paul K. 
Published: January 2021

Abstract
Objective: Maintaining adequate drug adherence is crucial to ensure the HIV prevention benefits of pre-exposure prophylaxis (PrEP). We developed an enzymatic assay for rapidly measuring tenofovir-diphosphate (TFV-DP) concentrations – a metabolite that indicates long-term PrEP adherence.Setting: The study was conducted at the Madison HIV Clinic at Harborview Medical Center in Seattle.Methods: We enrolled adults receiving standard oral PrEP, and individuals not receiving any antiretrovirals. We measured TFV-DP concentrations in diluted whole blood using our novel REverSe TRanscrIptase Chain Termination (RESTRICT) assay, based on inhibition of HIV reverse transcriptase (RT) enzyme. Blood samples were diluted in water, DNA templates, nucleotides, RT, and intercalating dye added, and results measured with a fluorescence reader—stronger fluorescence indicated higher RT activity. We compared RESTRICT assay results to TFV-DP concentrations from matched dried blood spot samples measured by liquid chromatography tandem mass spectrometry (LC-MS/MS) using ≥700 fmol/punch TFV-DP as a threshold for adequate adherence (≥4 doses/week).Results: Among 18 adults enrolled, 4 of 7 participants receiving PrEP had TFV-DP levels ≥700 fmol/punch by LC-MS/MS. RESTRICT fluorescence correlated with LC-MS/MS measurements (r=-0.845, p<0.0001). Median fluorescence was 93.3 (95% confidence interval [CI]: 90.9 to 114) for samples <700 fmol/punch and 54.4 (CI: 38.0 to 72.0) for samples ≥700 fmol/punch. When calibrated to an a priori defined threshold of 82.7, RESTRICT distinguished both groups with 100% sensitivity and 92.9% specificity. Conclusions: This novel enzymatic assay for measuring HIV reverse transcriptase activity may be suitable for distinguishing TFV-DP concentrations in blood that correspond to protective PrEP adherence.