bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historical fire in the Appalachian Plateau of Ohio and Kentucky, USA, from remnant yellow pines
Authors: Hutchinson Todd F. , Stambaugh Michael C. , Marschall Joseph M. , Guyette Richard P. 
Published: September 2019

AbstractBackgroundKnowledge of historical fire regimes informs the restoration of woodland communities. In the Appalachian Plateau of Ohio and Kentucky, USA, little is known about the long-term history of fire in oak–pine communities, which are declining in the region. To address this knowledge gap, two sites with remnant fire-scarred yellow pines, Hatton Ridge in Kentucky and McAtee Run in Ohio, were studied to document aspects of the historical fire regime. Cross-sections from fire-scarred yellow pines were collected. Fire chronologies were constructed and fire intervals were calculated using standard dendrochronological methods.ResultsFires, the great majority of which occurred in the dormant season, were frequent at both sites fromcirca1750 at Hatton and 1800 at McAtee, until the suppression period (1930 to present); only one fire was recorded after 1930. Mean fire intervals (MFI) for the entire period were nearly identical, 4.7 and 4.4 years at Hatton and McAtee, respectively. At both sites, MFIs were lowest in the industrial period (1850 to 1930). At Hatton, the MFI was 6.6 years before 1850 and 3.5 years from 1850 to 1930, while at McAtee, the MFI was 8.4 years before 1850 and 2.7 years from 1850 to 1930. At both sites, the occurrence of fire was not more frequent than expected in years associated with a drought. At McAtee, the majority of pine establishment occurred in pulses during two periods, 1770 to 1781 and 1853 to 1867, suggesting stand-scale canopy disturbances; the second pulse was associated with frequent burning. In contrast, large pulses of pine establishment were not found at Hatton.ConclusionsYellow pines were a component of these communities, which experienced frequent fire for at least 130 to 160 years. After more than 70 years with little or no fire, yellow pines are now a minor component of the overstory and pine regeneration is essentially absent. Although intensive management with partial harvesting and frequent fire would be required to restore oak–pine woodlands on appropriate sites, it would serve to sustain these increasingly uncommon communities.
Accuracy analysis of gradient reconstruction on isotropic unstructured meshes and its effects on inviscid flow simulation
Authors: Wang Nianhua , Li Ming , Ma Rong , Zhang Laiping 
Published: September 2019

AbstractThe accuracy of gradient reconstruction methods on unstructured meshes is analyzed both mathematically and numerically. Mathematical derivations reveal that, for gradient reconstruction based on the Green-Gauss theorem (the GG methods), if the summation of first-and-lower-order terms does not counterbalance in the discretized integral process, which rarely occurs, second-order accurate approximation of face midpoint value is necessary to produce at least first-order accurate gradient. However, gradient reconstruction based on the least-squares approach (the LSQ methods) is at least first-order on arbitrary unstructured grids. Verifications are performed on typical isotropic grid stencils by analyzing the relationship between the discretization error of gradient reconstruction and the discretization error of the face midpoint value approximation of a given analytic function. Meanwhile, the numerical accuracy of gradient reconstruction methods is examined with grid convergence study on typical isotropic grids. Results verify the phenomenon of accuracy degradation for the GG methods when the face midpoint value condition is not satisfied. The LSQ methods are proved to be at least first-order on all tested isotropic grids. To study gradient accuracy effects on inviscid flow simulation, solution errors are quantified using the Method of Manufactured Solutions (MMS) which was validated before adoption by comparing with an exact solution case, i.e., the 2-dimensional (2D) inviscid isentropic vortex. Numerical results demonstrate that the order of accuracy (OOA) of gradient reconstruction is crucial in determining the OOA of numerical solutions. Solution accuracy deteriorates seriously if gradient reconstruction does not reach first-order.
Antioxidant, anti-inflammatory and anticoagulant activities of three Thymus species grown in southeastern Morocco
Authors: Hmidani Abdelbassat , Bouhlali Eimad Dine Tariq , Khouya Tarik , Ramchoun Mhamed , Filali-Zegzouti Younes , Alem Chakib , Benlyas Mohamed 
Published: September 2019

Abstract

Background
Thyme has been used for centuries in southeastern Morocco to treat a wide range of diseases such as inflammation disorders. The aim of the current study is to examine and to compare in vitro the anti-inflammatory, antioxidant, and anticoagulant activities of three thyme species grown in southeastern Morocco.

Results
Data showed that all studied species possess an important antioxidant activity: Thymus atlanticus (IC50 = 16.59 μg/mL), Thymus zygis (IC50 = 15.43 μg/mL), and Thymus satureioides (IC50 = 14.65 μg/mL). Concerning the anti-inflammatory activity, the highest effect was depicted in Thymus atlanticus followed by Thymus zygis and Thymus satureioides. With regard to the anticoagulant activity, the aqueous extract of these species prolongs activated partial thromboplastin time, prothrombin time, and thrombin time significantly (p < 0.05) in a dose-dependent manner.

Conclusion
Our results provide evidence that thymus extract exhibits marked antioxidant, anticoagulant, and anti-inflammatory effects, thus justifying the popular uses of these plants to treat some inflammatory and cardiovascular illnesses.
Experimental model of peri-prosthetic infection of the knee caused by Staphylococcus aureus using biomaterials representative of modern TKA
Authors: Morris Jodie L. , Letson Hayley L. , Grant Andrea , Wilkinson Matthew , Hazratwala Kaushik , McEwen Peter 
Published: September 2019

ABSTRACT
Prosthetic joint infection (PJI) following total knee arthroplasty (TKA) remains the leading cause for revision surgery, with Staphylococcus aureus the bacterium most frequently responsible. We describe a novel rat model of implant-associated S. aureus infection of the knee using orthopaedic materials relevant to modern TKA. Male Sprague-Dawley rats underwent unilateral knee implant surgery, which involved placement of a cementless, porous titanium implant into the femur, and an ultra-highly cross-linked polyethyelene (UHXLPE) implant into the proximal tibia within a mantle of gentamicin-laden bone cement. S. aureus biofilms were established on the surface of titanium implants prior to implantation into the femur of infected animals, whilst control animals received sterile implants. Compared to controls, the time taken to full weight-bear and recover pre-surgical body weight was greater in the infected group. Neutrophils and C-reactive protein levels were significantly higher in infected compared to control animals at day 5 post surgery, returning to baseline levels for the remainder of the 28-day experimental period. Blood cultures remained negative and additional plasma inflammatory markers were comparable for control and infected animals, consistent with the clinical presentation of delayed-onset PJI. S. aureus was recovered from joint tissue and implants at day 28 post surgery from all animals that received pre-seeded titanium implants, despite the use of antibiotic-laden cement. Persistent localised infection was associated with increased inflammatory responses and radiological changes in peri-implant tissue. The availability of a preclinical model that is reproducible based on the use of current TKA materials and consistent with clinical features of delayed-onset PJI will be valuable for evaluation of innovative therapeutic approaches.
Feedback loops in the Plk4–STIL–HsSAS6 network coordinate site selection for procentriole formation
Authors: Takao Daisuke , Watanabe Koki , Kuroki Kanako , Kitagawa Daiju 
Published: September 2019

ABSTRACT
Centrioles are duplicated once in every cell cycle, ensuring the bipolarity of the mitotic spindle. How the core components cooperate to achieve high fidelity in centriole duplication remains poorly understood. By live-cell imaging of endogenously tagged proteins in human cells throughout the entire cell cycle, we quantitatively tracked the dynamics of the critical duplication factors: Plk4, STIL and HsSAS6. Centriolar Plk4 peaks and then starts decreasing during the late G1 phase, which coincides with the accumulation of STIL at centrioles. Shortly thereafter, the HsSAS6 level increases steeply at the procentriole assembly site. We also show that both STIL and HsSAS6 are necessary for attenuating Plk4 levels. Furthermore, our mathematical modeling and simulation suggest that the STIL-HsSAS6 complex in the cartwheel has a negative feedback effect on centriolar Plk4. Combined, these findings illustrate how the dynamic behavior of and interactions between critical duplication factors coordinate the centriole-duplication process.
This article has an associated First Person interview with the first author of the paper.
Escape responses of fish: a review of the diversity in motor control, kinematics and behaviour
Authors: Domenici Paolo , Hale Melina E. 
Published: September 2019

ABSTRACT
The study of fish escape responses has provided important insights into the accelerative motions and fast response times of these animals. In addition, the accessibility of the underlying neural circuits has made the escape response a fundamental model in neurobiology. Fish escape responses were originally viewed as highly stereotypic all-or-none behaviours. However, research on a wide variety of species has shown considerable taxon-specific and context-dependent variability in the kinematics and neural control of escape. In addition, escape-like motions have been reported: these resemble escape responses kinematically, but occur in situations that do not involve a response to a threatening stimulus. This Review focuses on the diversity of escape responses in fish by discussing recent work on: (1) the types of escape responses as defined by kinematic analysis (these include C- and S-starts, and single- versus double-bend responses); (2) the diversity of neuromuscular control; (3) the variability of escape responses in terms of behaviour and kinematics within the context of predator−prey interactions; and (4) the main escape-like motions observed in various species. Here, we aim to integrate recent knowledge on escape responses and highlight rich areas for research. Rapidly developing approaches for studying the kinematics of swimming motion both in the lab and within the natural environment provide new avenues for research on these critical and common behaviours.
The MELFO Study: A Multicenter, Prospective, Randomized Clinical Trial on the Effects of a Reduced Stage-Adjusted Follow-Up Schedule on Cutaneous Melanoma IB–IIC Patients—Results After 3 Years
Authors: Deckers Eric A. , Hoekstra-Weebers Josette E. H. M. , Damude Samantha , Francken Anne Brecht , ter Meulen Sylvia , Bastiaannet Esther , Hoekstra Harald J. 
Published: September 2019

Abstract

Background
This study compares well-being, recurrences, and deaths of early-stage cutaneous melanoma patients in follow-up, as recommended in the Dutch guideline, with that of patients in a stage-adjusted reduced follow-up schedule, 3 years after diagnosis, as well as costs.

Methods
Overall, 180 eligible pathological American Joint Committee on Cancer (AJCC) stage IB–IIC, sentinel node staged, melanoma patients (response rate = 87%, 48% male, median age 57 years), randomized into a conventional (CSG, n = 93) or experimental (ESG, n = 87) follow-up schedule group, completed patient-reported outcome measures (PROMs) at diagnosis (T1): State-Trait Anxiety Inventory–State version (STAI-S), Cancer Worry Scale (CWS), Impact of Event Scale (IES), and RAND-36 (Mental and Physical Component scales [PCS/MCS]). Three years later (T3), 110 patients (CSG, n = 56; ESG, n = 54) completed PROMs, while 42 declined (23%).

Results
Repeated measures analyses of variance (ANOVAs) showed a significant group effect on the IES (p = 0.001) in favor of the ESG, and on the RAND-36 PCS (p = 0.02) favoring the CSG. Mean IES and CWS scores decreased significantly over time, while those on the RAND-36 MCS and PCS increased. Effect sizes were small. Twenty-five patients developed a recurrence or second primary melanoma, of whom 13 patients died within 3 years. Cox proportional hazards models showed no differences between groups in recurrence-free survival (hazard ratio [HR] 0.71 [0.32–1.58]; p = 0.400) and disease-free survival (HR 1.24 [0.42–3.71]; p = 0.690). Costs per patient after 3 years (computed for 77.3% of patients) were 39% lower in the ESG.

Conclusion
These results seemingly support the notion that a stage-adjusted reduced follow-up schedule forms an appropriate, safe, and cost-effective alternative for pathological AJCC stage IB–IIC melanoma patients to the follow-up regimen as advised in the current melanoma guideline.
Use of social media in a national Tuberculosis Drug Resistance Survey: lessons from the first anti-tuberculosis drug resistance survey in Ghana
Authors: Sylverken Augustina Angelina , Owusu-Dabo Ellis , Kwarteng Alexander , Twumasi-Ankrah Sampson , Owusu Michael , Adu-Amoah Louis , Dumevi Rexford Mawunyo , Arthur Rejoice Agyeiwaa , Addofoh Nicholas , Dzata Francisca , Bonsu Frank 
Published: September 2019

Background: The widespread use of social media applications on mobile phones indicate that smart phones have become more than just a simple medium for voice calling. Several studies have shown the potential benefit of these social media applications in discussing many health conditions. We report on tracking sample transport by public and private transport providers using WhatsApp during the first nationwide drug resistance tuberculosis (TB) survey in Ghana. Methods: The survey was conducted between February 2016 and June 2017, and involved 33 TB diagnostic sites selected on the basis of a two-stage cluster randomized sampling design on both anticipated yield and probability proportional to size method. We engaged the services of privately and publicly owned vehicles’ union to transport samples to the Bacteriology department at the Kumasi Centre for Collaborative Research in Tropical Medicine laboratories for further laboratory processing. We created a mobile social group platform (‘National TBDRS’) on WhatsApp consisting of two representatives from each site as well as other stakeholders. The purpose was to notify a laboratory team in Kumasi, on the following details of the sample: date and time of dispatch, driver’s name, car number, estimated time of arrival, and bus terminal name. Results: A total 3077 WhatsApp messages were received during the survey period. Of these, 2879 (93.57%) messages were related to the survey. We observed a positive correlation between the total number of messages received and the total number of well-packaged sputum samples sent (r=0.89, p=0.02). There were no major transport delays (11:44±03:50) and all samples arrived within a 3-day window from the survey sites. Conclusions: Using WhatsApp as a platform of communication can aid in improving tracking of samples, enhance accountability of for example drivers handling the samples over at a road crossing and communication across health facilities.
Setting the stage for strengthened annual monitoring of family planning program performance at the state/national level in Myanmar
Authors: Nwe Tin Khaing , Williamson Jessica , Sonneveldt Emily 
Published: September 2019

Background: Although Myanmar has made good progress in family planning by increased contraceptive prevalence rate (CPR) from 41% in 2007 to 52.2% in 2016, it remains lower than the target of 60% by 2020. There are also huge disparities sub-nationally, ranging from 25% to 60%. While there is a strong need to monitor the progress of family planning program regularly at the national and sub-national level, Myanmar has limited surveys, data quality and methodological issues in its Health Management Information System (HMIS), and a scattered rollout of the Logistic Management Information System (LMIS). Methods: To identify viable options for annual monitoring, four data sources: modelled contraceptive prevalence rate for modern methods (mCPR) estimates from Track20’s Family Planning Estimation Tool (FPET); method-specific prevalence from the 2015-16 Myanmar Demographic and Health Survey (DHS); mCPR estimates and method prevalence from HMIS and estimates of modern method use (EMU) based on commodity consumption data from LMIS, were compared for the years 2015-2017. Estimates of mCPR from HMIS were tested for accuracy based on whether they fell within the 95% confidence interval of mCPR estimates from the FPET for the corresponding years. EMU from LMIS was also tested for those years and states/regions where available. Results: For annual tracking of mCPR, direct estimates of HMIS were considered carefully, as they were much higher than those of the DHS survey and were not matched by FPET results, except in Chin and Kayin. To monitor the method mix, HMIS data can be used as these are similar pattern with DHS in both national and State/Regional level except Chin and Kayin. LMIS could be used in annual tracking when there are high reporting rates and valid information of consumption. Conclusions: Track20’s FPET is the method of choice to get valid information for annual monitoring of family planning program.
Herniation of the caecum and ascending colon through the foramen of Winslow: a case report and review
Authors: Sammut M , Barben C 
Published: September 2019

Approximately 5% of intestinal obstruction cases are caused by internal herniation. Caecal herniation through the foramen of Winslow is considered a rare event. The management of caecal herniation remains challenging due to the lack of literature highlighting this pathology. A 66-year-old woman was admitted with a 24-hour history of epigastric pain radiating to the back. The pain was associated with nausea and vomiting of gastric contents. On examination, the abdomen was soft with mild tenderness but no signs of peritonism or distension. The abdominal x-ray and a computed tomography were in keeping with caecal volvulus and confirmed that the caecum was not in the right iliac fossa. In a midline laparotomy procedure, the ileum, caecum and ascending colon were noted to be herniating into the foramen of Winslow. A right hemicolectomy with a handsewn anastomosis was performed. The foramen of Winslow was not closed. No postoperative complications occurred. A literature review showed a lack of similar cases with no agreed management consensus. The laparotomy approach is comparable to the laparoscopic approach and no caecal herniation recurrence after open/laparoscopic surgical procedures were identified. Awareness of caecal herniation allows early diagnosis and timely surgical management is needed in prevent patient morbidity and mortality.
Automated verification of query equivalence using satisfiability modulo theories
Authors: Zhou Qi , Arulraj Joy , Navathe Shamkant , Harris William , Xu Dong 
Published: September 2019

Database-as-a-service offerings enable users to quickly create and deploy complex data processing pipelines. In practice, these pipelines often exhibit significant overlap of computation due to redundant execution of certain sub-queries. It is challenging for developers and database administrators to manually detect overlap across queries since they may be distributed across teams, organization roles, and geographic locations. Thus, we require automated cloud-scale tools for identifying equivalent queries to minimize computation overlap.
State-of-the-art algebraic approaches to automated verification of query equivalence suffer from two limitations. First, they are unable to model the semantics of widely-used SQL features, such as complex query predicates and three-valued logic. Second, they have a computationally intensive verification procedure. These limitations restrict their efficacy and efficiency in cloud-scale database-as-a-service offerings.
This paper makes the case for an alternate approach to determining query equivalence based on symbolic representation. The key idea is to effectively transform a wide range of SQL queries into first order logic formulae and then use satisfiability modulo theories to efficiently verify their equivalence. We have implemented this symbolic representation-based approach in EQUITAS. Our evaluation shows that EQUITAS proves the semantic equivalence of a larger set of query pairs compared to algebraic approaches and reduces the verification time by 27X. We also demonstrate that on a set of 17,461 real-world SQL queries, it automatically identifies redundant execution across 11% of the queries. Our symbolic-representation based technique is currently deployed on Alibaba's MaxCompute database-as-a-service platform.
DDSketch
Authors: Masson Charles , Rim Jee E. , Lee Homin K. 
Published: September 2019

Summary statistics such as the mean and variance are easily maintained for large, distributed data streams, but order statistics (i.e., sample quantiles) can only be approximately summarized. There is extensive literature on maintaining quantile sketches where the emphasis has been on bounding the rank error of the sketch while using little memory. Unfortunately, rank error guarantees do not preclude arbitrarily large relative errors, and this often occurs in practice when the data is heavily skewed.
Given the distributed nature of contemporary large-scale systems, another crucial property for quantile sketches is mergeablility, i.e., several combined sketches must be as accurate as a single sketch of the same data. We present the first fully-mergeable, relative-error quantile sketching algorithm with formal guarantees. The sketch is extremely fast and accurate, and is currently being used by Datadog at a wide-scale.
Adapting TPC-C benchmark to measure performance of multi-document transactions in MongoDB
Authors: Kamsky Asya 
Published: September 2019

MongoDB is a popular distributed database that supports replication, horizontal partitioning (sharding), a flexible document schema and ACID guarantees on the document level. While it is generally grouped with "NoSQL" databases, MongoDB provides many features similar to those of traditional RDBMS such as secondary indexes, an ad hoc query language, support for complex aggregations, and new as of version 4.0 multi-statement, multi-document ACID transactions.
We looked for a well understood OLTP workload benchmark to use in our own system performance test suite to establish a baseline of transaction performance to enable flagging performance regressions, as well as improvements as we continue to add new functionality. While there exist many published and widely used benchmarks for RDBMS OLTP workloads, there are none specifically for document databases.
This paper describes the process of adapting an existing traditional RDBMS benchmark to MongoDB query language and transaction semantics to allow measuring transaction performance. We chose to adapt the TPC-C benchmark even though it assumes a relational database schema and SQL, hence extensive changes had to be made to stay consistent with MongoDB best practices. Our goal did not include creating official TPC-C certifiable results, however, every attempt was made to stay consistent with the spirit of the original benchmark specification as well as to be compliant to all specification requirements where possible.
We discovered that following best practices for document schema design achieves better performance than using required normalized schema. All the source code used and validation scripts are published in github to allow the reader to recreate and verify our results.