bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioreduction in the development of new mineral technology
Authors: Pawlowska A , Sadowski Z 
Published: November 2019

Abstract
Reductive dissolution is like “biomining in reverse gear”. Selected sulfur reducing bacteria (SRB) can be used under anaerobic conditions – as in bioleaching – for metal recovery from oxide minerals and laterite. General assumptions of the BioSulphide® and Ferredox processes for nickel recovery from laterite ores and copper from acid mine drainage or waste water were presented.
Extraction, Production and Consumption of Gravel and Sand Aggregates in Poland An Attempt to Assess National and Regional Balances
Authors: Kozioł W , Baic I 
Published: November 2019

Abstract
Natural aggregates are the basic group of extracted minerals. In Poland, their share in the extraction of solid minerals over 30 years (1989–2018) increased from about 24% to 54%. Current aggregate production is about 300 million Mg and in 2019 it will probably exceed the record volume of 2011 – over 330 million Mg. In the extraction and production of aggregates in Poland, there is a decisive preponderance of gravel and sand aggregates – their share in the total production of natural aggregates amounts to 70–75%. The remaining part consists of crushed-stone aggregates produced from compact and moderately compact rocks of magma origin (basalts, granites, gabbro and diabases, melaphyres, porphyry, syenites, etc.), sedimentary rocks (dolomites, limestones, sandstones, etc.), and metamorphic rocks (amphibolites, migamatites, gneisses, serpentinites, etc.). A gradual deterioration in the quality of the raw material base of gravel and sands as well as a simultaneous increase in the demand of the construction industry for the best quality thick aggregate fractions (5/8mm, 8/11, etc.) has a significant impact on the rise in the amount of hard to sell and unsalable (waste) fractions of aggregates produced in Poland. This applies especially to gravel and sand aggregates in whose deposit the share of fine fractions (below 2 mm) is systematically increasing, while the demand for them in the construction sector is limited and they are often treated as useless (waste) material. Since it is practically unknown what is the production and consumption of these aggregates, an attempt was made to assess the amount of extracted and produced sand and gravel fractions of natural aggregates in Poland.
The deficit of natural aggregates in many countries and regions as well as the limited aggregate resources in Poland and increasing difficulties in obtaining licenses for their extraction indicate the need for selective storage of sand aggregate assortments instead of “melting” them in post-mining excavation pits. The presented research results should contribute to the development of more accurate market forecasts regarding the demand for and production of natural aggregates in Poland and in individual regions, especially when it comes to gravel and sand aggregates, including also fine fractions.
Prediction of mutation effects using a deep temporal convolutional network
Authors: Kim Ha Young , Kim Dongsup 
Published: November 2019

Abstract

Motivation
Accurate prediction of the effects of genetic variation is a major goal in biological research. Towards this goal, numerous machine learning models have been developed to learn information from evolutionary sequence data. The most effective method so far is a deep generative model based on the variational autoencoder (VAE) that models the distributions using a latent variable. In this study, we propose a deep autoregressive generative model named mutationTCN, which employs dilated causal convolutions and attention mechanism for the modeling of inter-residue correlations in a biological sequence.

Results
We show that this model is competitive with the VAE model when tested against a set of 42 high-throughput mutation scan experiments, with the mean improvement in Spearman rank correlation ∼0.023. In particular, our model can more efficiently capture information from multiple sequence alignments with lower effective number of sequences, such as in viral sequence families, compared with the latent variable model. Also, we extend this architecture to a semi-supervised learning framework, which shows high prediction accuracy. We show that our model enables a direct optimization of the data likelihood and allows for a simple and stable training process.

Availability and implementation
Source code is available at https://github.com/ha01994/mutationTCN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Natural killer cells: functional differences in recurrent spontaneous abortion†
Authors: Hao Fan , Zhou Xiangyu , Jin Liping 
Published: November 2019

AbstractRecurrent spontaneous abortion (RSA) is one of the major pregnancy disorders and poses a serious risk to both the mother and the fetus. Although a number of research efforts have been conducted, therapeutic advances for treating RSA have not lived up to their expectations. Hence, other treatments should be explored. The important role of natural killer (NK) cells in immunotherapy is attracting increasing attention, both as a pharmaceutical target and for cell therapies. NK cells are abundant in the endometrium and play a role in implantation and placentation in normal pregnancy. As research progresses, NK cells are increasingly regarded as playing essential roles in the emergence and development of RSA. In this article, I review recent findings on the role of uterine NK cells in the pathophysiology of RSA. These cells may become therapeutic NK cell-related targets. In conclusion, although several issues regarding NK cells in RSA remain unresolved and require further investigation, extensive evidence is available for the treatment of RSA.
Adaptive response of extreme epiphyte Tillandsia species (Bromeliaceae) is demonstrated by different sexual reproduction strategies in the Brazilian Chaco
Authors: Gomes Aline C , Ferreira Bruno H S , Souza Camila S , Arakaki Luan M M , Aoki Camila , Paggi Gecele Matos , Sigrist Maria Rosângela 
Published: November 2019

AbstractSome epiphytes are adapted to extreme environments with the ability to survive drought as a result of their morphological (xeromorphism), anatomical (foliar trichomes or scales) and physiological features. In contrast to vegetative features, they may have diverse sexual reproductive strategies. Here we compared the flowering morphology, floral biology, breeding system and pollinators of Tillandsia duratii, T. loliacea and T. recurvifolia (Bromeliaceae) adapted to an extreme environment, the Brazilian Chaco. Tillandsia duratii and T. recurvifolia flower for 5–6 months, whereas T. loliaceae flowers for 11 months, mainly in the dry season, with low to high flowering overlap between them. Although these species generally show similar flowering morphology, they differ in size, colour, odour and/or floral functionality, suggesting non-sharing of pollinators among them. Bimodal pollination occurs in T. duratii (bees, moths other than hawkmoths) and T. recurvifolia (butterflies, hummingbirds); in T. loliacea, we recorded no floral visitors. Tillandsia recurvifolia is self-incompatible, has flowers which approach herkogamy and protandry, and depends on pollen vectors for fruit set. The other two species show reverse herkogamy, autonomous self-pollination and self-compatibility (mixed breeding system); therefore, pollinators are not required. The disparity in reproductive strategies among the three species suggests the possibility of selection for diverse modes of reproduction.
The impact of volume overload on technique failure in incident peritoneal dialysis patients
Authors: Vrtovsnik François , Verger Christian , Van Biesen Wim , Fan Stanley , Shin Sug-Kyun , Rodríguez Carmen , Garcia Méndez Isabel , van der Sande Frank M , De los Ríos Tatiana , Ihle Katharina , Gauly Adelheid , Ronco Claudio , Heaf James ,   for the IPOD-PD Study Group
Published: November 2019

Abstract

Background
Technique failure in peritoneal dialysis (PD) can be due to patient- and procedure-related factors. With this analysis, we investigated the association of volume overload at the start and during the early phase of PD and technique failure.

Methods
In this observational, international cohort study with longitudinal follow-up of incident PD patients, technique failure was defined as either transfer to haemodialysis or death, and transplantation was considered as a competing risk. We explored parameters at baseline or within the first 6 months and the association with technique failure between 6 and 18 months, using a competing risk model.

Results
Out of 1092 patients of the complete cohort, 719 met specific inclusion and exclusion criteria for this analysis. Being volume overloaded, either at baseline or Month 6, or at both time points, was associated with an increased risk of technique failure compared with the patient group that was euvolaemic at both time points. Undergoing treatment at a centre with a high proportion of PD patients was associated with a lower risk of technique failure.

Conclusions
Volume overload at start of PD and/or at 6 months was associated with a higher risk of technique failure in the subsequent year. The risk was modified by centre characteristics, which varied among regions.
Evaluation of additional benefits of HPV vaccination to cervical cancer screening in France
Authors: Rousseau S , Massetti M , Barre S , Leleu H , Gaillot-de Saintignon J 
Published: November 2019

Abstract

Background
The National Cancer Institute (INCa) undertook the evaluation of the expected impact of HPV vaccination in the context of the recent marketing of nonavalent vaccine (Gardasil®9) and the implementation of organized screening (OS) of cervical cancer (CC) in France.

Methods
The study is based on a microsimulation model that replicates the natural history of CC. A cohort of 14-year-old women is generated and followed until death. Others HPV-infection related diseases (condyloma, anal cancer, penile cancer and oropharynx cancer) are not modelled. Different strategies were compared with the current vaccination coverage rate (VCR) of 21.4% (2017): impact of increased VCR alone and increased VCR combined with correction of inequalities (CI). Results are presented according to two hypotheses for the duration of protection offered by the vaccine (limited to 20 years and lifelong) and according to two hypotheses for price of the vaccine (French price and average European prices).

Results
The incremental cost-effectiveness ratio (ICER) was less than 15 000 euros per QALY (quality-adjusted life year) in all the assessed strategies. For each 14-year-old women cohort, 85% VCR with CI would prevent at least: 2 546 conations, 2 347 precancerous lesions CIN 2 / 3 diagnosed, 377 CCs, 139 deaths per CC (20 years vaccine protection). Scenarios based on increasing VCR with CI are the most cost-effective.

Conclusions
The study quantifies the increased risk of CC-related outcomes associated with current sub-optimal VCR and the possible investment to implement actions in order to improve the efficiency of the current strategies and tackle health inequalities (communication campaign, actions toward underserved women).

Key messages
Improving HPV vaccination uptake is a cost-effective measure, even considering only the cervical cancer prevention. Including health inequalities participation in modeling is crucial as underserved women are both less vaccinated and screened.
School ethos and recurring sickness absence: a multilevel study of ninth grade students in Stockholm
Authors: Låftman S Brolin , Ramberg J , Modin B 
Published: November 2019

Abstract

Background
A non-negligible proportion of Swedish students is recurrently absent from school due to various health problems. Recurring absence from school has potentially severe consequences for future prospects. Thus, identifying factors that may contribute to counteracting recurring sickness absence among students is important. The aim of this study was to investigate whether higher levels of teacher-reported school ethos were associated with lower levels of recurring sickness absence among their students, when adjusting for relevant confounders at the student- and the school-level.

Methods
Data from four cross-sectional surveys performed in 2014 and 2016 were combined. The Stockholm School Survey was carried out among 9,298 ninth grade students (ages 15-16 years) in 147 school units, and the Stockholm Teacher Survey was performed among 2,024 teachers in the same units. School ethos was captured by an index of 12 teacher-reported items that was aggregated to the school-level. Recurring student sickness absence was based on self-reports and defined as absence on &gt; 10 occasions during the current school year. Student-level control variables were gender, family structure, parental education, parental unemployment and migration background. School-level control variables were sociodemographic composition and student-teacher ratio. Two-level logistic regressions were performed.

Results
About 9.5% of the students reported recurrent sickness absence. Students attending schools with higher levels of teacher-rated school ethos had a lower likelihood of reporting recurring sickness absence compared with those attending schools with lower levels of ethos, even when adjusting for potential confounders at the student- and the school-level (OR 0.78, p = 0.015).

Conclusions
Recurring sickness absence was less common among students attending schools with higher levels of teacher-rated ethos. The findings suggest that schools have the capacity to promote student health.

Key messages
A strong school ethos was linked with lower levels of recurring sickness absence among the students, even when adjusting for potential confounders at the student- and the school-level. A strong school ethos may contribute to counteracting recurring sickness absence among students.
RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements
Authors: Osipova Ekaterina , Hecker Nikolai , Hiller Michael 
Published: November 2019

Abstract

Background
Transposons and other repetitive sequences make up a large part of complex genomes. Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty. However, comprehensively detecting ancestral repeats that align between species is difficult because considering all repeat-overlapping seeds in alignment methods that rely on the seed-and-extend heuristic results in prohibitively high runtimes.

Results
Here, we show that ignoring repeat-overlapping alignment seeds when aligning entire genomes misses numerous alignments between repetitive elements. We present a tool, RepeatFiller, that improves genome alignments by incorporating previously undetected local alignments between repetitive sequences. By applying RepeatFiller to genome alignments between human and 20 other representative mammals, we uncover between 22 and 84 Mb of previously undetected alignments that mostly overlap transposable elements. We further show that the increased alignment coverage improves the annotation of conserved non-exonic elements, both by discovering numerous novel transposon-derived elements that evolve under constraint and by removing thousands of elements that are not under constraint in placental mammals.

Conclusions
RepeatFiller contributes to comprehensively aligning repetitive genomic regions, which facilitates studying transposon co-option and genome evolution. Source code: https://github.com/hillerlab/GenomeAlignmentTools
March-ing toward organizational economics
Authors: Gibbons Robert 
Published: November 2019

Abstract
I was a student of Jim March’s in 1983, meaning that I took a mandatory 10-week doctoral class on organization theory from him that changed my life. And I have been a student of Jim’s ever since, meaning that I have tried to keep learning from Jim’s ideas—about organizations and about life. During the course and for over a decade afterwards, most of my academic learning from Jim was about how disciplines other than economics think about organizations. More recently, I have tried to discern how the roots of my own field, organizational economics, often involve Jim. This note focuses on the latter, especially informed by precious summer discussions from 2013 to 2018.1
Images and Memory: Religiosity and Sacrifice – The Cases of Tierralta, Trujillo and Arenillo in Colombia
Authors: Guerrero Freddy A , López Aristizabal Liza 
Published: November 2019

Abstract
Memory in Colombia is a human right that is recognized for victims and society in the framework of processes of transitional justice, and in the last decade there has been an institutionalization of memory, with organizations arising whose purpose is to manage memory initiatives in the country. However, organizational and community memory and denunciation processes and practices have been developed, materialized and represented through objects/images, like sources and references for memory aimed to account for the atrocious past and promote acts of resistance and humanity amid the inhumanity of war. From a fragmentary perspective, we concentrate on three cases of images in Colombia that, based on religious and cultural representations, allow us to observe their power in processes of recovering memory, of denunciation and demands with regard to respect for human rights.
Essential numerical ranges for linear operator pencils
Authors: Bögli Sabine , Marletta Marco 
Published: November 2019

Abstract
We introduce concepts of essential numerical range for the linear operator pencil $\lambda \mapsto A-\lambda B$. In contrast to the operator essential numerical range, the pencil essential numerical ranges are, in general, neither convex nor even connected. The new concepts allow us to describe the set of spectral pollution when approximating the operator pencil by projection and truncation methods. Moreover, by transforming the operator eigenvalue problem $Tx=\lambda x$ into the pencil problem $BTx=\lambda Bx$ for suitable choices of $B$, we can obtain nonconvex spectral enclosures for $T$ and, in the study of truncation and projection methods, confine spectral pollution to smaller sets than with hitherto known concepts. We apply the results to various block operator matrices. In particular, Theorem 4.12 presents substantial improvements over previously known results for Dirac operators while Theorem 4.5 excludes spectral pollution for a class of nonselfadjoint Schrödinger operators which has not been possible to treat with existing methods.
Maternal nutrition during early and late gestation in gilts and sows under commercial conditions: impacts on maternal growth and litter traits1
Authors: Mallmann André L , Fagundes Deivison P , Vier Carlos E , Oliveira Gabriela S , Mellagi Ana P G , Ulguim Rafael R , Bernardi Mari L , Orlando Uislei A D , Cogo Ricardo J , Bortolozzo Fernando P 
Published: November 2019

Abstract
The effects of two different feeding levels, offered in two phases during gestation, on body measurements and litter traits were evaluated in 152 gilts and 551 sows. The treatments consisted of the combination of two gestation phases (phase 1—days 22 to 42; phase 2—days 90 to 110) and two feed amounts (1.8 or 3.5 kg/d). Females were weighed on days 22, 42, 90, and 110 of gestation. Born alive and stillborn piglets were weighed within 12 h of birth. Total placental efficiency (ratio between litter weight and total placental weight) was measured in 518 females. Variables concerning body measurements at days 42 and 90 of gestation were analyzed considering the effects of feed amount, parity order (PO) and its interaction as a 2 × 2 factorial arrangement. Body measurements at day 110 of gestation and litter traits were analyzed considering the effects of feed amounts in phase 1, feed amounts in phase 2, PO and their interactions, as a 2 × 2 × 2 factorial arrangement. As expected, BW, backfat, and caliper units were greater at days 42, 90, and 110 (P ≤ 0.006) for females fed 3.5 kg/d during the previous phase than those fed 1.8 kg. No differences were observed among feed levels in total number of piglets born, mummified fetuses, sum of born alive and stillborn piglets, and within-litter birth weight CV (P ≥ 0.118). The percentage of stillborn piglets was affected by a three-way interaction (feed level at phase 1 × feed level at phase 2 × PO). Gilts fed 1.8 kg/d at phase 1 and 3.5 kg/d at phase 2 had fewer stillborn piglets than the other females (P ≤ 0.004). Birth weight was not affected by feed levels (P ≥ 0.153); however, sows had heavier piglets than gilts (P &lt; 0.001). Females fed 3.5 kg/d during phase 2 tended to have heavier litters (P = 0.054) than those fed 1.8 kg/d. Feeding a high level at phase 2 reduced the occurrence of lightweight piglets in gilts, but not in sows (feed level phase 2 × PO; P = 0.031). Total placental weight, average placental weight, and total placental efficiency were not affected by feed level at phase 1, feed level at phase 2 or interactions (P &gt; 0.14). Sows had total placental weight and average placental weight greater (P ≤ 0.003) than gilts. In conclusion, increasing feed intake during phase 1, phase 2, or both phases resulted in increased maternal BW gain, without expressive effects on litter traits. Feeding 3.5 kg/d to gilts during phase 2 reduced the occurrence of lightweight piglets.
High-Throughput UHPLC-MS/MS Measurement of Per- and Poly-Fluorinated Alkyl Substances in Human Serum
Authors: Mottaleb M Abdul , Petriello Michael C , Morris Andrew J 
Published: November 2019

Abstract
Per- and poly-fluorinated alkyl substances (PFASs) are a large group of synthetic surfactant chemicals with widespread uses in food packaging and textile manufacturing and as the main constituent of aqueous film-forming firefighting foams. PFASs are highly persistent in the environment, and human exposures are extensive with these chemicals detectable in the blood of almost all adult Americans. PFASs exhibit a range of toxic effects in preclinical models. In humans, PFAS exposure has been associated with lower birth weights, decreased immune responses, cancer and impaired fertility and elevated circulating cholesterol levels. We have developed a sensitive high-throughput method for quantification of representative PFAS in human serum and plasma for biomonitoring and epidemiological studies of human health effects of PFAS exposure. The method combines robust and reproducible 96-well plate format sample preparation with ultra-performance liquid chromatography–tandem mass spectrometry. The method was developed, validated and used for targeted measurements of eight short-/long-chain PFAS analytes in human serum. Targeted analytes were measured in 50 microliters of sample using mass-labeled internal standards. Mean spiked recoveries (n = 10) of target analytes for three tiers quality control (QC-low, QC-medium, QC-high) samples ranged from 70 to 127% with 2–14% relative standard deviation (RSD). The average spiked recoveries (n = 10) of surrogates were 79–115% with 8–12% RSD for QC-low, 90–123% with 7–12% RSD for QC-medium and 82–114% with 9–15% RSD for QC-high. The limit of detection for the target compounds was 0.05–0.04 ng/mL. The method was used to reveal regional differences in PFAS exposures in Kentucky residents receiving care at the University of Kentucky Hospitals.