bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIM-based real time building energy simulation and optimization in early design stage
Authors: Gao Hao , Zhang Liwenbo , Koch Christian , Wu Yupeng 
Published: August 2019

AbstractIncreasing requirements of sustainability has prompted architects to pay more attention to the energy performance of their design. The design decisions, such as building form, orientation, window size, and construction materials, made in the early design stages have the significant impact on the building energy performance. However, architects who has limited knowledge of energy modelling usually suffer from selecting and using the common building energy simulation tools. Consequently, building energy simulations are rarely used in the early design process. It is imperative to develop a tool integrated with the deisgn tool to help architect to understand the effects of various design stratigies on building energy performance. Fortunately, the simplified building energy calculation method and Building Information Modelling (BIM) provide an innovative approach for architect. In this paper, a BIM-based real time building energy simulation and optimization tool is proposed and developed based on quasi-steady state method, Revit API and Dynamo, which can assist architects to optimize the building form, building orientation and window to wall ratio (WWR) based on building energy performance in the early design stage to provide better stratigeis for buildings energy efficient design.
Supply Chain Management of the Plywood Industry in Indonesia
Authors: Makkarennu  , Natsir H R , Supratman  
Published: August 2019

Abstract
The plywood industry in Indonesia experienced a heyday in the 1980s and experienced ups and downs in the following year. One of the causes of the decline in plywood production in several industries is the supply chain management of raw materials. This study aims to determine supply chain mechanisms related to the flow of product, flow of financial and flow of information at the plywood industry in South Sulawesi. Data collection techniques are carried out with initial observations, field surveys, interviews, and literature studies. Data analysis was performed using qualitative and quantitative descriptive analysis. The results show that the supply chain in plywood mills has a fairly complex link starting from product flow, financial flow and information flow related to raw material supply, inventory and sales. This company needs to implement an integrated supply chain management to help maintain the sustainability of plywood production so as to increase the company’s performance.
Neutron imaging analysis using jupyter Python notebook
Authors: Bilheux Jean-Christophe , Bilheux Hassina , Lin Jiao , Lumsden Ian , Zhang Yuxuan 
Published: August 2019

Abstract
Independently of the image modality (x-rays, neutrons, etc), image data analysis requires normalization, a preprocessing step. While the normalization can sometimes easily be generalized, the analysis is, in most cases, specific to an experiment and a sample. Although many tools (MATLAB, ImageJ, VG Studio…) offer a large collection of pre-programmed image analysis tools, they usually require a learning step that can be lengthy depending on the skills of the end user. We have implemented Jupyter Python notebooks to allow easy and straightforward data analysis, along with live interaction with the data. Jupyter notebooks require little programming knowledge and the steep learning curve is bypassed. Most importantly, each notebook can be tailored to a specific experiment and sample with minimized effort. Here, we present the pros and cons of the main methods to analyse data and show the reason why we have found that Jupyter Python notebooks are well suited for imaging data processing, visualization and analysis.
Geographic Information System (GIS)-Based Mapping and Spatial Analyses Applied to Risk Assessment and Resource Allocation for Boll Weevil (Coleoptera: Curculionidae) Detection
Authors: Brewer Michael J , Deleon Leonel , Esquivel Isaac L 
Published: August 2019

Abstract
Boll weevil, Anthonomous grandis grandis Boheman first invaded U.S. cotton in Texas in the late 1800s, and spread throughout U.S. cotton-growing regions by the 1920s. Boll weevil eradication efforts initiated in the eastern United States in the 1980s resulted in its elimination except in the southernmost region of Texas and adjoining areas of Mexico. We focused on geographic information system (GIS)-based mapping and spatial analyses of boll weevil trap data to consider whether landscape features were associated with spatially variable detections of boll weevils. Seven years of trap data were overlaid with data layers of vector-based classifications of cropland, transportation, and hydrological features. New boll weevil detections in 2018 were 108 km north of cotton fields in the Lower Rio Grande Valley (LRGV) where more persistent detections occurred. Focusing on LRGV data, 14 of 24 correlations of number of boll weevil captures to nearest distances to selected landscape features were negative. In follow-up analyses, best data fit was seen using stepwise regression. In 2010, waterbodies and watermelon fields were influential linear terms (partial R2 = 0.14 and 0.064, respectively; model R2 = 0.32). In 2014, the Rio Grande River as a linear term was influential (partial R2 = 0.15; model R2 = 0.24). Boll weevil captures tended to increase in closer proximity to these landscape features. Results of 2010 were consistent with expectations of remnant populations in the LRGV spreading locally, while 2014 results may reflect remnant populations or re-introductions from boll weevil moving longer distances into the LRGV.
Male mate choice for large gravid spots in a livebearing fish
Authors: Ogden Hannah J P , de Boer Raïssa A , Devigili Alessandro , Reuland Charel , Kahrl Ariel F , Fitzpatrick John L 
Published: August 2019

AbstractMale mate choice occurs in a wide range of species, and males can increase their reproductive success by distinguishing between females based on their fecundity (e.g., large body size) or their expected sperm competition risk (e.g., virgins). However, patterns of male mate choice could be mitigated by variation in female physiological receptivity, as males can benefit by directing their mating efforts toward females that are at a point in their reproductive cycle when fertilization probability is highest. Here, we perform three experiments to assess whether male mate choice is influenced by cues of female physiological receptivity, fecundity, or sperm competition risk in the pygmy halfbeak (Dermogenys collettei), a small livebearing fish. Female halfbeaks possess a “gravid spot”—an orange abdominal marking that is caused by pigmentation of the females’ skin and variation in embryo development and pigmentation during pregnancy. We show that gravid spot size increases toward parturition and is largest right before giving birth, independent of abdominal width or body size. Males consistently chose females with large gravid spots over females with small gravid spots. In contrast, males did not prefer larger females over smaller females or virgin females over mated females. As female halfbeaks store sperm prior to fertilizations, we suggest that males use the size of the gravid spot as a cue to direct their mating efforts to those females where the chance of fertilization is highest.
MeLAD: an integrated resource for metalloenzyme-ligand associations
Authors: Li Gen , Su Yu , Yan Yu-Hang , Peng Jia-Yi , Dai Qing-Qing , Ning Xiang-Li , Zhu Cheng-Long , Fu Chen , McDonough Michael A , Schofield Christopher J , Huang Cheng , Li Guo-Bo 
Published: August 2019

Abstract

Motivation
Metalloenzymes are attractive targets for therapeutic intervention owing to their central roles in various biological processes and pathological situations. The fast-growing body of structural data on metalloenzyme-ligand interactions is facilitating efficient drug discovery targeting metalloenzymes. However, there remains a shortage of specific databases that can provide centralized, interconnected information exclusive to metalloenzyme-ligand associations.

Results
We created a Metalloenzyme-Ligand Association Database (MeLAD), which is designed to provide curated structural data and information exclusive to metalloenzyme-ligand interactions, and more uniquely, present expanded associations that are represented by metal-binding pharmacophores (MBPs), metalloenzyme structural similarity (MeSIM) and ligand chemical similarity (LigSIM). MeLAD currently contains 6086 structurally resolved interactions of 1416 metalloenzymes with 3564 ligands, of which classical metal-binding, non-classical metal-binding, non-metal-binding and metal water-bridging interactions account for 63.0%, 2.3%, 34.4% and 0.3%, respectively. A total of 263 monodentate, 191 bidentate and 15 tridentate MBP chemotypes were included in MeLAD, which are linked to different active site metal ions and coordination modes. 3726 and 52 740 deductive metalloenzyme-ligand associations by MeSIM and LigSIM analyses, respectively, were included in MeLAD. An online server is provided for users to conduct metalloenzyme profiling prediction for small molecules of interest. MeLAD is searchable by multiple criteria, e.g. metalloenzyme name, ligand identifier, functional class, bioinorganic class, metal ion and metal-containing cofactor, which will serve as a valuable, integrative data source to foster metalloenzyme related research, particularly involved in drug discovery targeting metalloenzymes.

Availability and implementation
MeLAD is accessible at https://melad.ddtmlab.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Causal inference with confounders missing not at random
Authors: Yang S , Wang L , Ding P 
Published: August 2019

Summary
It is important to draw causal inference from observational studies, but this becomes challenging if the confounders have missing values. Generally, causal effects are not identifiable if the confounders are missing not at random. In this article we propose a novel framework for nonparametric identification of causal effects with confounders subject to an outcome-independent missingness, which means that the missing data mechanism is independent of the outcome, given the treatment and possibly missing confounders. We then propose a nonparametric two-stage least squares estimator and a parametric estimator for causal effects.
Effectiveness of Acellular Pertussis Vaccine in Older Adults: Nested Matched Case-control Study
Authors: Liu Bette C , He Wen-Qiang , Newall Anthony T , Quinn Helen E , Bartlett Mark , Hayen Andrew , Sheppeard Vicky , Rose Nectarios , Macintyre C Raina , Mcintyre Peter 
Published: August 2019

Abstract

Background
Despite recommendations that older adults receive acellular pertussis vaccines, data on direct effectiveness in adults aged over 50 years are sparse.

Methods
A case-control study nested within an adult cohort. Cases were identified from linked pertussis notifications and each matched to 3 controls on age, sex, and cohort recruitment date. Cases and controls were invited to complete a questionnaire, with verification of vaccination status by their primary care provider. Vaccine effectiveness (VE) was estimated by conditional logistic regression, with adjustment for reported contact with children and area of residence.

Results
Of 1112 notified cases in the cohort, we had complete data for 333 cases and 506 controls. Among 172 PCR-diagnosed cases (mean age, 61 years), 11.2% versus 19.5% of controls had provider-verified pertussis vaccination, on average, 3.2 years earlier. Adjusted VE against PCR-diagnosed pertussis was 52% (95% CI, 15–73%), nonsignificantly higher if vaccinated within 2 years (63%; −5–87%). Adjusted VE was similar in adults born before 1950, presumed primed by natural infection (51%; −8–77%) versus those born 1950 or later who may have received whole-cell pertussis vaccine (53%; −11–80%) (P-heterogeneity = 0.9). Among 156 cases identified by single-point serology, adjusted VE was −55% (−177–13%).

Conclusions
We found modest protection against PCR-confirmed pertussis among older adults (mean age, 61 years; range, 46–81 years) within 5 years after acellular vaccine. The most likely explanation for the markedly divergent VE estimate from cases identified by single-titer serology is misclassification arising from limited diagnostic specificity in our setting.
Transcatheter aortic valve implantation versus surgical aortic valve replacement in low-risk patients: a propensity score-matched analysis
Authors: Schaefer Andreas , Schofer Niklas , Goßling Alina , Seiffert Moritz , Schirmer Johannes , Deuschl Florian , Schneeberger Yvonne , Voigtländer Lisa , Detter Christian , Schaefer Ulrich , Blankenberg Stefan , Reichenspurner Hermann , Conradi Lenard , Westermann Dirk 
Published: August 2019

Abstract

OBJECTIVES
The aim of the study was to determine the differences in outcomes of surgical aortic valve replacement (SAVR) and transcatheter aortic valve implantation (TAVI) in low-risk patients.

METHODS
All patients with a logistic EuroSCORE II <4% who underwent transfemoral TAVI between 2008 and 2016 (n = 955) or SAVR between 2009 and 2014 (n = 886) at our centre were included. One hundred and nine patients per group were available for propensity score matching.

RESULTS
Mortality during the 30-day follow-up showed no differences (SAVR vs TAVI: 1.1% vs 1.8%, P = 1.0) but the rates of permanent pacemaker implantation (0.0 vs 14.8%, P < 0.001) and paravalvular leakage ≥ moderate (0.0 vs 7.0%, P = 0.017) were higher in TAVI patients. No difference was found regarding postoperative effective orifice area and transvalvular pressure gradients. Although, the 1-year survival was similar between both groups; 3- and 5-year survival was significantly inferior in the TAVI patient cohort.

CONCLUSIONS
TAVI yielded similar short-term outcomes compared with SAVR despite higher rates of permanent pacemaker implantation and paravalvular leakage ≥ moderate, but inferior long-term survival. Poorer long-term outcomes of the TAVI patient cohort were attributable to a more comorbid TAVI population. This emphasizes the need for long-term results from randomized controlled trials before TAVI can be broadly expanded to younger low-risk patients.
Vacuum-formed retainer versus bonded retainer for dental stabilization in the mandible—a randomized controlled trial. Part I: retentive capacity 6 and 18 months after orthodontic treatment
Authors: Krämer Anke , Sjöström Mats , Hallman Mats , Feldmann Ingalill 
Published: August 2019

Summary

Background
Evidence concerning the most appropriate retention strategy after orthodontic treatment is still inconclusive.

Objective
This trial compares the retentive capacity of vacuum-formed Essix C-retainers (VFR) and bonded cuspid-to-cuspid retainers (CTC) in the mandible 6 and 18 months after orthodontic treatment.

Trial design
A single-centre two-arm parallel-group randomized controlled trial.

Methods
This study included 104 adolescent patients, computer-generated randomized with sequentially numbered, opaque, and sealed envelopes into two groups and stratified by gender (52 females and 52 males). The patients were treated with fixed appliances with and without tooth extractions in both jaws and were ready for debond. In the intervention arm, patients received a VFR (n = 52); in the active comparator arm, patients received a CTC (n = 52). Dental casts were obtained at debond (T1), after 6 months (T2), and after 18 months (T3). The casts were digitized. The retentive capacity was evaluated on digital three-dimensional models using Little’s Irregularity Index (LII), overbite, overjet, arch length, and intermolar and intercanine width.

Results
Baseline values were similar for both groups. Statistically significant increases were noted in LII and overbite, mainly between T1 and T2, but also between T1 and T3 in the VFR group (LII = 0.52 mm, P &lt; 0.001, overbite = 0.51 mm, P &lt; 0.001) and in the CTC group (LII = 0.45 mm P &lt; 0.001, overbite = 0.36 mm, P &lt; 0.001). There were no significant differences between groups. Overjet showed small variations during the observation periods but was overall stable within and between groups after 18 months. Arch length decreased slightly in both groups after 6 and 18 months. Intermolar and intercanine widths remained stable after debond.

Limitations
Patients, operator, and outcome assessor could not be blinded due to the study design.

Conclusions
VFR and CTC have the same retention capacity in the mandible after 6 and 18 months. Relapse mainly occurs during the first 6 months of retention, but the post-treatment changes are generally small. Shorter VFRs in the mandible do not cause negative vertical effects. Part-time wear regimen is not associated with increased relapse.

Trial registration
NCT03070444.
Biogeographical patterns in soil bacterial communities across the Arctic region
Authors: Malard Lucie A , Anwar Muhammad Z , Jacobsen Carsten S , Pearce David A 
Published: August 2019

ABSTRACT
The considerable microbial diversity of soils and key role in biogeochemical cycling have led to growing interest in their global distribution and the impact that environmental change might have at the regional level. In the broadest study of Arctic soil bacterial communities to date, we used high-throughput DNA sequencing to investigate the bacterial diversity from 200 independent Arctic soil samples from 43 sites. We quantified the impact of spatial and environmental factors on bacterial community structure using variation partitioning analysis, illustrating a nonrandom distribution across the region. pH was confirmed as the key environmental driver structuring Arctic soil bacterial communities, while total organic carbon (TOC), moisture and conductivity were shown to have little effect. Specialist taxa were more abundant in acidic and alkaline soils while generalist taxa were more abundant in acidoneutral soils. Of the 48 147 bacterial taxa, a core microbiome composed of only 13 taxa that were ubiquitously distributed and present within 95% of samples was identified, illustrating the high potential for endemism in the region. Overall, our results demonstrate the importance of spatial and edaphic factors on the structure of Arctic soil bacterial communities.
A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata
Authors: Liu Qin , Guo Yunhai , Zhang Yi , Hu Wei , Li Yuanyuan , Zhu Dan , Zhou Zhengbin , Wu Jiatong , Chen Nansheng , Zhou Xiao-Nong 
Published: August 2019

Abstract

Background
Triatoma rubrofasciata is a widespread pathogen vector for Chagas disease, an illness that affects approximately 7 million people worldwide. Despite its importance to human health, its evolutionary origin has not been conclusively determined. A reference genome for T. rubrofasciata is not yet available.

Finding
We have sequenced the genome of a female individual with T. rubrofasciatausing a single molecular DNA sequencing technology (i.e., PacBio Sequel platform) and have successfully reconstructed a whole-genome (680-Mb) assembly that covers 90% of the nuclear genome (757 Mb). Through Hi-C analysis, we have reconstructed full-length chromosomes of this female individual that has 13 unique chromosomes (2n = 24 = 22 + X1 + X2) with a contig N50 of 2.72 Mb and a scaffold N50 of 50.7 Mb. This genome has achieved a high base-level accuracy of 99.99%. This platinum-grade genome assembly has 12,691 annotated protein-coding genes. More than 95.1% of BUSCO genes were single-copy completed, indicating a high level of completeness of the genome.

Conclusion
The platinum-grade genome assembly and its annotation provide valuable information for future in-depth comparative genomics studies, including sexual determination analysis in T. rubrofasciata and the pathogenesis of Chagas disease.
Energy efficient cooling and heating of aquaponics facilities based on regional climate
Authors: Alkhalidi Ammar , Khawaja Mohamad K , Abusubaih Dana 
Published: August 2019

Abstract
An already existing aquaponics facility in Jordan, named Khodra, will be used to evaluate the cooling and heating profiles to provide the best environment for plants and fish to thrive. A replica of the ‘Khodra’ facility will be simulated to be built in Qatar. Good ventilation rate with 50% green color shading was sufficient to reduce the temperature down by almost 10 degrees in ‘Khodra’-Jordan while using a heating, ventilation and air conditioning water-chiller based system reduced the humidity in the ‘Khodra’-Qatar greenhouse yet using AC split units was cheaper for the small size, 360 m2, of this specific greenhouse.
Inferior vena cava resection without reconstruction for retroperitoneal malignancies
Authors: Cocchi Lorenzo , Di Domenico Stefano , Bertoglio Sergio , Treppiedi Elio , Ficarra Gianluca , De Cian Franco 
Published: August 2019

ABSTRACT
Inferior vena cava (IVC) involvement in retroperitoneal malignancies is a rare occurrence and radical surgery with major vascular resection represents the only potential curative treatment. IVC replacement after resection is still controversial and only small series and few prospective data are available. We report a series of three patients affected by retroperitoneal masses involving IVC treated with vena cava resection without replacement. All patients were treated by a radical R0 surgical procedure associated with infrarenal IVC resection and no reconstruction. Based on preoperative radiologic imaging and intraoperative findings, one patient also underwent right nephrectomy, while another patient underwent left renal vein ligation without nephrectomy. Neither early nor late severe post-operative complications related to the absence of IVC outflow were observed. Resection without replacement of the infrarenal IVC results in acceptable morbidity, thus specific risks related to the use of prosthetic grafts can be avoided.
The redshift evolution of X-ray and Sunyaev–Zel’dovich scaling relations in the fable simulations
Authors: Henden Nicholas A , Puchwein Ewald , Sijacki Debora 
Published: August 2019

Abstract
We study the redshift evolution of the X-ray and Sunyaev–Zel’dovich (SZ) scaling relations for galaxy groups and clusters in the fable suite of cosmological hydrodynamical simulations. Using an expanded sample of 27 high-resolution zoom-in simulations, together with a uniformly sampled cosmological volume to sample low-mass systems, we find very good agreement with the majority of observational constraints up to z ∼ 1. We predict significant deviations of all examined scaling relations from the simple self-similar expectations. While the slopes are approximately independent of redshift, the normalizations evolve positively with respect to self-similarity, even for commonly used mass proxies such as the YX parameter. These deviations are due to a combination of factors, including more effective active galactic nuclei feedback in lower mass haloes, larger binding energy of gas at a given halo mass at higher redshifts, and larger non-thermal pressure support from kinetic motions at higher redshifts. Our results have important implications for cluster cosmology from upcoming SZ surveys such as SPT-3G, ACTpol, and CMB-S4, as relatively small changes in the observable–mass scaling relations (within theoretical uncertainties) have a large impact on the predicted number of high-redshift clusters and hence on our ability to constrain cosmology using cluster abundances. In addition, we find that the intrinsic scatter of the relations, which agrees well with most observational constraints, increases at lower redshifts and for lower mass systems. This calls for a more complex parametrization than adopted in current observational studies to be able to accurately account for selection biases.