bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fiber-optic sensor measuring spatial distributions of refractive index and temperature
Authors: Pfalzgraf Ivonne , Suntsov Sergiy , Kip Detlef 
Published: January 2021

In this work, we present a fiber sensor designed to measure simultaneously spatial inhomogeneities of the refractive index and temperature in liquid media, for example, induced by biochemical reactions. The sensor’s constituent elements are Fabry–Perot microresonators fabricated in standard single-mode optical fibers by diamond blade dicing. To allow simultaneous measurements of different refractive indices, the sensor comprises two open cavities approximately 2 mm apart. With a small Si inlay inserted into one of the resonators used for temperature measurements, the sensor allows for immediate compensation of crosstalk between temperature- and composition-induced fluids’ refractive index changes. The measurements were evaluated by phase tracking of the characteristic Fourier transform components of the sensor’s backreflected spectra. The temperature sensitivity of the Si inlay is 0.063 rad/°C (79 pm/°C), and an accuracy of 0.01°C is obtained. Meanwhile, the two refractive index sensing (open) cavities show a sensitivity of 1168 and 1153 nm/RIU for temperature-compensated measurements. Finally, the sensor performance to measure spatial distributions is demonstrated by measuring the diffusion behavior of sucrose in water, which allows precise monitoring of hydration effects and breaking of bonds at elevated temperatures.
Realization of directional single-mode lasing by a GaN-based warped microring
Authors: Zhang Shengnan , Li Yufeng , Hu Peng , Tian Zhenhuan , Li Qiang , Li Aixing , Zhang Ye , Yun Feng 
Published: January 2021

Multimode and random directionalities are major issues restricting the application of whispering gallery mode microcavity lasers. We demonstrated a 40 μm diameter microring with an off-centered embedded hole and warped geometry from strained III-nitride quantum well multilayers. Single-mode directional whispering gallery mode lasing was achieved by the warped structure and high-order mode suppression induced by the off-centered hole. In addition, the introduction of the off-centered hole reduced the lasing threshold from 3.24 to

2.79

MW
/
cm

2

compared with the warped microdisk without an embedded hole while maintaining a high-quality factor of more than 4000. Directional light emission in 3D was achieved and attributed to the warped structure, which provides a vertical component of the light emission, making it promising for building multifunctional coherent light sources in optoelectronic integration.
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
Authors: Sundermann Linda K. , Wintersinger Jeff , Rätsch Gunnar , Stoye Jens , Morris Quaid 
Published: January 2021

Tumors contain multiple subpopulations of genetically distinct cancer cells. Reconstructing their evolutionary history can improve our understanding of how cancers develop and respond to treatment. Subclonal reconstruction methods cluster mutations into groups that co-occur within the same subpopulations, estimate the frequency of cells belonging to each subpopulation, and infer the ancestral relationships among the subpopulations by constructing a clone tree. However, often multiple clone trees are consistent with the data and current methods do not efficiently capture this uncertainty; nor can these methods scale to clone trees with a large number of subclonal populations.
Here, we formalize the notion of a partially-defined clone tree (partial clone tree for short) that defines a subset of the pairwise ancestral relationships in a clone tree, thereby implicitly representing the set of all clone trees that have these defined pairwise relationships. Also, we introduce a special partial clone tree, the Maximally-Constrained Ancestral Reconstruction (MAR), which summarizes all clone trees fitting the input data equally well. Finally, we extend commonly used clone tree validity conditions to apply to partial clone trees and describe SubMARine, a polynomial-time algorithm producing the subMAR, which approximates the MAR and guarantees that its defined relationships are a subset of those present in the MAR. We also extend SubMARine to work with subclonal copy number aberrations and define equivalence constraints for this purpose. Further, we extend SubMARine to permit noise in the estimates of the subclonal frequencies while retaining its validity conditions and guarantees. In contrast to other clone tree reconstruction methods, SubMARine runs in time and space that scale polynomially in the number of subclones.
We show through extensive noise-free simulation, a large lung cancer dataset and a prostate cancer dataset that the subMAR equals the MAR in all cases where only a single clone tree exists and that it is a perfect match to the MAR in most of the other cases. Notably, SubMARine runs in less than 70 seconds on a single thread with less than one Gb of memory on all datasets presented in this paper, including ones with 50 nodes in a clone tree. On the real-world data, SubMARine almost perfectly recovers the previously reported trees and identifies minor errors made in the expert-driven reconstructions of those trees.
The freely-available open-source code implementing SubMARine can be downloaded at https://github.com/morrislab/submarine.
Insecticide-treated house screening protects against Zika-infected Aedes aegypti in Merida, Mexico
Authors: Manrique-Saide Pablo , Herrera-Bojórquez Josué , Medina-Barreiro Anuar , Trujillo-Peña Emilio , Villegas-Chim Josué , Valadez-González Nina , Ahmed Ahmed M. M. , Delfín-González Hugo , Palacio-Vargas Jorge , Che-Mendoza Azael , Pavía-Ruz Norma , Flores Adriana E. , Vazquez-Prokopec Gonzalo 
Published: January 2021

Background
The integration of house-screening and long-lasting insecticidal nets, known as insecticide-treated screening (ITS), can provide simple, safe, and low-tech Aedes aegypti control. Cluster randomised controlled trials in two endemic localities for Ae. aegypti of south Mexico, showed that ITS conferred both, immediate and sustained (~2 yr) impact on indoor-female Ae. aegypti infestations. Such encouraging results require further validation with studies quantifying more epidemiologically-related endpoints, including arbovirus infection in Ae. aegypti. We evaluated the efficacy of protecting houses with ITS on Ae. aegypti infestation and arbovirus infection during a Zika outbreak in Merida, Yucatan, Mexico.

Methodology/Principal findings
A two-arm cluster-randomised controlled trial evaluated the entomological efficacy of ITS compared to the absence of ITS (with both arms able to receive routine arbovirus vector control) in the neighbourhood Juan Pablo II of Merida. Cross-sectional entomological surveys quantified indoor adult mosquito infestation and arbovirus infection at baseline (pre-ITS installation) and throughout two post-intervention (PI) surveys spaced at 6-month intervals corresponding to dry/rainy seasons over one year (2016–2017). Household-surveys assessed the social reception of the intervention. Houses with ITS were 79–85% less infested with Aedes females than control houses up to one-year PI. A similar significant trend was observed for blood-fed Ae. aegypti females (76–82%). Houses with ITS had significantly less infected female Ae. aegypti than controls during the peak of the epidemic (OR = 0.15, 95%CI: 0.08–0.29), an effect that was significant up to a year PI (OR = 0.24, 0.15–0.39). Communities strongly accepted the intervention, due to its perceived mode of action, the prevalent risk for Aedes-borne diseases in the area, and the positive feedback from neighbours receiving ITS.

Conclusions/Significance
We show evidence of the protective efficacy of ITS against an arboviral disease of major relevance, and discuss the relevance of our findings for intervention adoption.
Space-time risk cluster of visceral leishmaniasis in Brazilian endemic region with high social vulnerability: An ecological time series study
Authors: Ribeiro Caique J. N. , dos Santos Allan D. , Lima Shirley V. M. A. , da Silva Eliete R. , Ribeiro Bianca V. S. , Duque Andrezza M. , Peixoto Marcus V. S. , dos Santos Priscila L. , de Oliveira Iris M. , Lipscomb Michael W. , de Araújo Karina C. G. M. , de Moura Tatiana R. 
Published: January 2021

BackgroundDespite visceral leishmaniasis (VL) being epidemic in most Brazilian regions, the Northeast region is responsible for the highest morbidity and mortality outcomes within the country.ObjectiveTo analyse the spatiotemporal dynamics of VL cases to identify the temporal trends and high-risk areas for VL transmission, as well as the association of the disease with social vulnerability in Brazilian Northeast.MethodsWe carried out an ecological time series study employing spatial analysis techniques using all VL confirmed cases of 1,794 municipalities of Brazilian Northeast between the years 2000 to 2017. The Social Vulnerability Index (SVI) was used to represent the social vulnerability. Incidence rates were standardized and smoothed by the Local Empirical Bayesian Method. Time trends were examined through segmented linear regression. Spatiotemporal analysis consisted of uni- and bivariate Global and Local Moran indexes and space-time scan statistics.ResultsIncidence rate remained stable and ranged from 4.84 to 3.52 cases/100,000 inhabitants. There was higher case prevalence between males (62.71%), children and adolescents (63.27%), non-white (69.75%) and urban residents (62.58%). Increasing trends of new cases were observed among adult male subjects (≥ 40 years old) and urban residents. Importantly, VL incidence showed a direct spatial dependence. Spatial and space-time clusters were identified insertãoandmeio-nortesub-regions, overlapping with high social vulnerability areas.ConclusionsVL is a persistent health issue in Brazilian Northeast and associated with social vulnerability. Space-time clustering of VL cases in socially vulnerable municipalities demands intersectoral public policies of surveillance and control, with focus on reducing inequalities and improving living conditions for regional inhabitants.
“I wish to remain HIV negative”: Pre-exposure prophylaxis adherence and persistence in transgender women and men who have sex with men in coastal Kenya
Authors: Kimani Makobu , van der Elst Elise M. , Chirro Oscar , Wahome Elizabeth , Ibrahim Fauz , Mukuria Nana , de Wit Tobias F. Rinke , Graham Susan M. , Operario Don , Sanders Eduard J. 
Published: January 2021

BackgroundTransgender women (TGW) and men who have sex with men (MSM) in sub-Saharan Africa have high HIV acquisition risks and can benefit from daily pre-exposure prophylaxis (PrEP). We assessed PrEP adherence by measuring tenofovir-diphosphate (TFV-DP) levels and explore motives for PrEP persistence in TGW and MSM.MethodsParticipants were enrolled in a one-year PrEP programme and made quarterly visits irrespective of whether they were still using PrEP. At their month 6 visit, participants provided a dried blood spot to test for TFV-DP levels; protective levels were defined as those compatible with ≥4 pills per week (700–1249 fmol/punch). Before TFV-DP levels were available, a sub-set of these participants were invited for an in-depth interview (IDI). Semi-structured IDI topic guides were used to explore motives to uptake, adhere to, and discontinue PrEP. IDI data were analyzed thematically.ResultsFifty-three participants (42 MSM and 11 TGW) were enrolled. At month 6, 11 (20.7%) participants (8 MSM and 3 TGW) were lost to follow up or stopped taking PrEP. Any TFV-DP was detected in 62.5% (5/8) of TGW vs. 14.7% of MSM (5/34, p = 0.01). Protective levels were detected in 37.5% of TGW (3/8), but not in any MSM. Nineteen IDI were conducted with 7 TGW and 9 MSM on PrEP, and 1 TGW and 2 MSM off PrEP. Unplanned or frequent risky sexual risk behaviour were the main motives for PrEP uptake. Among participants on PrEP, TGW had a more complete understanding of the benefits of PrEP. Inconsistent PrEP use was attributed to situational factors. Motives to discontinue PrEP included negative reactions from partners and stigmatizing healthcare services.ConclusionWhile MSM evinced greater adherence challenges in this PrEP programme, almost 40% of TGW were protected by PrEP. Given high HIV incidences in TGW these findings hold promise for TGW PrEP programming in the region.
Value of endoscopic ultrasonography in the observation of the remnant pancreas after pancreatectomy
Authors: Maruyama Hirotsugu , Hanada Keiji , Shimizu Akinori , Minami Tomoyuki , Hirano Naomiti , Hino Fumiaki , Abe Tomoyuki , Amano Hironobu , Fujiwara Yasuhiro 
Published: January 2021

Background
Endoscopic ultrasonography (EUS) is proven to be a more specific and sensitive method for detecting pancreatic lesions. However, usefulness of EUS after pancreatectomy has not been reported. This study aimed to evaluate the observational capability of EUS for the remnant pancreas (RP) after pancreatectomy.

Patient and methods
This single-center, retrospective study enrolled 395 patients who underwent pancreatectomy at Onomichi General Hospital between December 2002 and March 2016, 45 patients who underwent EUS for RP were included for analysis. We evaluated the usefulness of EUS for RP using logistic regression analysis.

Results
Complete observation of the RP was done in 42 patients (93%). In the initial surgical procedure, 21 patients underwent pancreaticoduodenectomy (PD), and 24 patients underwent distal pancreatectomy (DP). PD and DP were observed in 85% (18/21) and 100% (24/24) cases, respectively. A comparison of the detection capability of EUS and contrast-enhanced computed tomography (CT) or magnetic resonance imaging (MRI) showed that EUS was significantly superior to contrast-enhanced CT or MRI (p < 0.01). Eight of the 45 patients showed recurrence lesions in the RP. The median recurrence period was 33 months. Predictive factors for recurrence in the univariate and multivariate analyses were significantly different in space occupying lesion with EUS findings (p < 0.01) and elevated CA19-9(p < 0.01).

Conclusions
EUS was able to observe the RP in almost all cases. In addition, the detection capability of EUS was significantly superior to those of CT or MRI. We recommend that all patients with RP should undergo EUS, and a longer follow-up must be performed.
Cannabis sativa subsp. sativa’s pharmacological properties and health effects: A scoping review of current evidence
Authors: Lim Xin Yi , Tan Terence Yew Chin , Muhd Rosli Siti Hajar , Sa’at Muhammad Nor Farhan , Sirdar Ali Syazwani , Syed Mohamed Ami Fazlin 
Published: January 2021

IntroductionHemp (Cannabis sativasubsp.sativa), commonly used for industrial purposes, is now being consumed by the public for various health promoting effects. As popularity of hemp research and claims of beneficial effects rises, a systematic collection of current scientific evidence on hemp’s health effects and pharmacological properties is needed to guide future research, clinical, and policy decision making.ObjectiveTo provide an overview and identify the present landscape of hemp research topics, trends, and gaps.MethodsA systematic search and analysis strategy according to the preferred reporting items for systematic review and meta-analysis-ScR (PRISMA-ScR) checklist on electronic databases including MEDLINE, OVID (OVFT, APC Journal Club, EBM Reviews), Cochrane Library Central and Clinicaltrials.gov was conducted to include and analyse hemp research articles from 2009 to 2019.Results65 primary articles (18 clinical, 47 pre-clinical) were reviewed. Several randomised controlled trials showed hempseed pills (in Traditional Chinese Medicine formulation MaZiRenWan) improving spontaneous bowel movement in functional constipation. There was also evidence suggesting benefits in cannabis dependence, epilepsy, and anxiety disorders. Pre-clinically, hemp derivatives showed potential anti-oxidative, anti-hypertensive, anti-inflammatory, anti-diabetic, anti-neuroinflammatory, anti-arthritic, anti-acne, and anti-microbial activities. Renal protective effects and estrogenic properties were also exhibitedin vitro.ConclusionCurrent evidence on hemp-specific interventions are still preliminary, with limited high quality clinical evidence for any specific therapeutic indication. This is mainly due to the wide variation in test item formulation, as the multiple variants of this plant differ in their phytochemical and bioactive compounds. Future empirical research should focus on standardising the hemp plant for pharmaceutical use, and uniformity in experimental designs to strengthen the premise of using hemp in medicine.
Balancing time use for children’s fitness and adiposity: Evidence to inform 24-hour guidelines for sleep, sedentary time and physical activity
Authors: Dumuid Dorothea , Wake Melissa , Burgner David , Tremblay Mark S. , Okely Anthony D. , Edwards Ben , Dwyer Terence , Olds Timothy 
Published: January 2021

Purpose
Daily time spent on one activity cannot change without compensatory changes in others, which themselves may impact on health outcomes. Optimal daily activity combinations may differ across outcomes. We estimated optimal daily activity durations for the highest fitness and lowest adiposity.

Methods
Cross-sectional Child Health CheckPoint data (1182 11-12-year-olds; 51% boys) from the population-based Longitudinal Study of Australian Children were used. Daily activity composition (sleep, sedentary time, light physical activity [LPA], moderate-to-vigorous physical activity [MVPA]) was from 8-day, 24-hour accelerometry. We created composite outcomes for fitness (VO2max; standing long jump) and adiposity (waist-to-height ratio; body mass index; fat-to-fat-free log-ratio). Adjusted compositional models regressed activity log-ratios against each outcome. Best activity compositions (optimal time-use zones) were plotted in quaternary tetrahedrons; the overall optimal time-use composition was the center of the overlapping area.

Results
Time-use composition was associated with fitness and adiposity (all measures p<0.001). Optimal time use differed for fitness and adiposity. While both maximized MVPA and minimized sedentary time, optimal fitness days had higher LPA (3.4 h) and shorter sleep (8.25 h), but optimal adiposity days had lower LPA (1.0 h) and longer sleep (10.9 h). Balancing both outcomes, the overall optimal time-use composition was (mean [range]): 10.2 [9.5; 10.5] h sleep, 9.9 [8.8; 11.2] h sedentary time, 2.4 [1.8; 3.2] h LPA and 1.5 [1.5; 1.5] h MVPA.

Conclusion
Optimal time use for children’s fitness and adiposity involves trade-offs. To best balance both outcomes, estimated activity durations for sleep and LPA align with, but for MVPA exceed, 24-h guidelines.
Chronic kidney disease and the outcomes of fibrinolysis for ST-segment elevation myocardial infarction: A real-world study
Authors: Xie Wuxiang , Patel Anushka , Boersma Eric , Feng Lin , Li Min , Gao Runlin , Wu Yangfeng 
Published: January 2021

Background
In low-resource regions, fibrinolytic therapy is often the only option for ST-elevation myocardial infarction (STEMI) patients as primary percutaneous coronary intervention (PCI) is often not available and patients are hardly transferred to a medical center with PCI capacity within the first 120 minutes. Chronic kidney disease (CKD) is one of the most frequently encountered complications of STEMI. However, the evidence for the efficacy of fibrinolytic therapy in STEMI patients with CKD is still limited. The aim of this study is to test whether CKD modifies the association between fibrinolytic therapy and short-term major adverse cardiovascular events (MACEs) among patients with STEMI.

Methods and findings
This is a real-world study analyzing the data from 9508 STEMI patients (mean age: 64.0±12.4 years; male: 70.1%) in the third phase of Clinical Pathways in Acute Coronary Syndromes program (CPACS-3), which is a large study of the management of acute coronary syndromes (ACS) in 101 county hospitals without PCI capacity in China. CKD was defined as an estimated glomerular filtration rate of less than 60 mL/min per 1·73 m2 at the admission. The primary outcome is short-term MACEs, including all-cause death, recurrent myocardial infarction, or nonfatal stroke. Patients were recruited consecutively between October 2011 and November 2014. Out of them, 1282 patients (13.5%) were classified as having CKD. Compared with non-CKD patients, CKD patients were less likely to receive fibrinolytic therapy than non-CKD patients (26.4% vs. 38.9%, P<0.001), more likely to experience a failed fibrinolytic therapy (32.8% vs. 16.9%), and had a higher risk of short-term MACEs (19.7% vs. 5.6%). After full adjustment, use of fibrinolytic therapy was associated with a significantly lower risk of short-term MACEs in non-CKD patients (relative risk [RR] = 0.87, 95% confidence interval [CI]: 0.76–0.99), but not in CKD patients (P for interaction = 0.026). Further analysis stratified by the success of fibrinolysis showed that compared with patients who did not receive fibrinolytic therapy, patients with successful fibrinolysis had a lower risk of short-term MACEs that was similar between patients with (RR = 0.71, 95% CI: 0.55–0.82) and without CKD (RR = 0.67, 95% CI: 0.55–0.92), while patients with unsuccessful fibrinolysis had a similarly higher risk in CKD patients (RR = 1.25, 95% CI: 1.09–1.43) and non-CKD patients (RR = 1.30, 95% CI: 1.13–1.50).

Conclusions
CKD reduced the likelihood of successful fibrinolysis and increased the risk of short-term MACEs in patients with STEMI. Attention should be paid to how to improve the success rate of fibrinolytic therapy for STEMI patients with CKD.

Trial registration
The CPACS-3 study was registered on www.clinicaltrials.gov (NCT01398228).
AGRO-INDUSTRIAL REGIONS: DYNAMICS OF INCOME, INEQUALITY AND POVERTY
Authors: Sergienko A.M. 
Published: January 2021

The results of the analysis of long-term dynamics of income, inequality and poverty in Russian agro-industrial regions are presented. The methodological background of the study is described. The specificity of changes in the considered indicators of development of agro-industrial regions against the background of Russia is revealed at different stages of economic development in the 1990s, 2000s and in the current decade. The agro-industrial regions consistently have lower incomes compared to Russia, higher levels of poverty and less significant inequalities. The impact of economic crises on the decline in the purchasing power of incomes and on the increase in poverty of residents in such regions was more noticeable than in Russia as a whole. At the same time, over more than 20 years, poverty has significantly decreased, purchasing power increased, and the regions’ lagging behind in terms of population income and overtaking in terms of poverty has decreased. Conclusions are drawn about the importance of state policy as a driver of positive changes in the dynamics of the population income and poverty in the agro-industrial regions.
It is shown how interregional differentiation changed. The “leading” and “outsider” agro-industrial regions are identified at each stage of economic development. There are significant and growing differences between agroindustrial regions in terms of income, inequality and poverty. The influence of the center-periphery factor on the position of regions is revealed. The position of the peripheral region with the least prosperous situation remains stable. The stability of the positions of the peripheral region with the least favorable situation remains. The group of prosperous regions (despite the change in leadership positions) with a more advantageous geographical position is also relatively stable.