bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water quality assessment of Cisadane River using pollution indicator parameters
Authors: Purwati Sri Unon , Lestari Nastiti Sih , Nasution Eva Lindasari 
Published: December 2019

Abstract
The Cisadane River catchment area is approximately 1,375.43 km2, and it is one of the main rivers in Banten and West Java Province, Indonesia. The Cisadane River has an important function in supporting the lives of many people with all their activities. Most of the studies related to the assessment of the water resources quality have used through several water quality indices, Those are are water quality index (WQI), water pollution index (WPI), and river habitat survey (RHS). However, the study of determining pollutant sources in the river has less done, including Cisadane River in this case. This study aimed to identify the important environmental parameters that can be used as indicators of pollution in the Cisadane River. This research was conducted in 2007 - 2014 by collecting water samples, 2 - 4 times every year. Employing the box and whisker statistical method, it can be concluded that free chlorine (Cl2), biological oxygen demand (BOD), chemical oxygen demand (COD), phenol, total coliform and E.coli were reliable indicators of contamination in The Cisadane River. As an indicator of pollution in the Cisadane River 6 these parameters can be used as a basis for assessing the quality of Cisadane water.
Calling in the face of danger: Do nestling Red-winged Blackbirds (Agelaius phoeniceus) suppress begging in response to predator playbacks?
Authors: Yasukawa Ken , Sollenberger Jessica , Lindsey-Robbins Josie , DeBruyn Elizabeth 
Published: December 2019

AbstractNest predation is the most frequent cause of nest failure in birds such as the Red-winged Blackbird (Agelaius phoeniceus) that nest on or near the substrate. Nestlings should therefore exhibit adaptations to reduce the risk of nest predation. We tested the nestling antipredator hypothesis by examining the begging responses of Red-winged Blackbird nestlings to vocalizations of (1) an important nest predator (American Crow, Corvus brachyrhynchos), (2) a predator that rarely preys on nestlings (Cooper’s Hawk, Accipiter cooperii), and (3) a nonpredator (Northern Flicker, Colaptes auratus). We performed playbacks with (1) both parents present at the nest, (2) male at the nest, and (3) neither parent present. Following playback, we measured duration of nestling begging after the parent departed (begging persistence), bouts of otherwise normal begging when no parent was present (parent-absent begging), and calling without postural components of begging (nonpostural begging). When the male or both parents were present during playback, adults responded with alarm calls and nestlings significantly reduced parent-absent begging following American Crow and Cooper’s Hawk playbacks. Nonpostural begging was significantly reduced following Cooper’s Hawk playback, but there were no significant differences in the other begging variables. When neither parent was present, we found no significant differences in nonpostural begging in response to the 3 playback types, but parent-absent begging was significantly reduced following American Crow and Cooper’s Hawk playbacks when compared to Northern Flicker playbacks. These results show that nestlings suppress their vocal begging in response to calls of predators including Cooper’s Hawks even though they are not common nest predators.
Deep learning for drug response prediction in cancer
Authors: Baptista Delora , Ferreira Pedro G , Rocha Miguel 
Published: December 2019

AbstractPredicting the sensitivity of tumors to specific anti-cancer treatments is a challenge of paramount importance for precision medicine. Machine learning(ML) algorithms can be trained on high-throughput screening data to develop models that are able to predict the response of cancer cell lines and patients to novel drugs or drug combinations. Deep learning (DL) refers to a distinct class of ML algorithms that have achieved top-level performance in a variety of fields, including drug discovery. These types of models have unique characteristics that may make them more suitable for the complex task of modeling drug response based on both biological and chemical data, but the application of DL to drug response prediction has been unexplored until very recently. The few studies that have been published have shown promising results, and the use of DL for drug response prediction is beginning to attract greater interest from researchers in the field. In this article, we critically review recently published studies that have employed DL methods to predict drug response in cancer cell lines. We also provide a brief description of DL and the main types of architectures that have been used in these studies. Additionally, we present a selection of publicly available drug screening data resources that can be used to develop drug response prediction models. Finally, we also address the limitations of these approaches and provide a discussion on possible paths for further improvement. Contact: mrocha@di.uminho.pt
RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures
Authors: Richardson Katherine E , Kirkpatrick Charles C , Znosko Brent M 
Published: December 2019

Abstract
The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, database is a freely accessible online database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure database; it now has the capability of analyzing, comparing and summarizing search results.
Database URL: http://rnacossmos.com
PCaLiStDB: a lifestyle database for precision prevention of prostate cancer
Authors: Chen Yalan , Liu Xingyun , Yu Yijun , Yu Chunjiang , Yang Lan , Lin Yuxin , Xi Ting , Ye Ziyun , Feng Zhe , Shen Bairong 
Published: December 2019

AbstractThe interaction between genes, lifestyles and environmental factors makes the genesis and progress of prostate cancer (PCa) very heterogeneous. Positive lifestyle is important to the prevention and controlling of PCa. To investigate the relationship between PCa and lifestyle at systems level, we established a PCa related lifestyle database (PCaLiStDB) and collected the PCa-related lifestyles including foods, nutrients, life habits and social and environmental factors as well as associated genes and physiological and biochemical indexes together with the disease phenotypes and drugs. Data format standardization was implemented for the future Lifestyle-Wide Association Studies of PCa (PCa_LWAS). Currently, 2290 single-factor lifestyles and 856 joint effects of two or more lifestyles were collected. Among these, 394 are protective factors, 556 are risk factors, 45 are no-influencing factors, 52 are factors with contradictory views and 1977 factors are lacking effective literatures support. PCaLiStDB is expected to facilitate the prevention and control of PCa, as well as the promotion of mechanistic study of lifestyles on PCa.Database URL: http://www.sysbio.org.cn/pcalistdb/
Larval Performance of a Major Forest Pest on Novel Hosts and the Effect of Stressors
Authors: Peterson Donnie L , Cipollini Don 
Published: December 2019

AbstractNovel hosts lacking a coevolutionary history with herbivores can often support improved larval performance over historic hosts; e.g., emerald ash borer [Agrilus planipennis (Fairmaire) Coleoptera: Buprestidae] on North American ash (Fraxinus spp.) trees. Whether trees are novel or ancestral, stress on plants increases emerald ash borer preference and performance. White fringetree [Chionanthus virginicus (L.) Lamiales: Oleaceae] and olive [Olea europaea (L.) Lamiales: Oleaceae] are closely related non-ash hosts that support development of emerald ash borer to adulthood, but their relative suitability as hosts and the impact of plant stress on larval success has not been well studied. In a series of experiments, survival and growth of emerald ash borer larvae on these novel hosts were examined along with the impact of stress. In the first experiment, larvae grew more slowly in cut stems of olive than in green ash [Fraxinus pennsylvanica (Marshall) Lamiales: Oleaceae] and several adults successfully emerged from larger olive stems. In two experiments on young potted olive with photosynthesizing bark, larvae died within a week, but mechanical girdling increased the rate of gallery establishment. The final two experiments on field-grown fringetrees found increased larval survivorship and growth in previously emerald ash borer attacked and mechanically girdled plants than in healthy stems or stems treated with the defense hormone, methyl jasmonate. Our results demonstrate that these non-ash hosts are less suitable for emerald ash borer than preferred ash hosts, but previous emerald ash borer attack or girdling led to better survival and growth demonstrating the importance of stress for larval success. In potted olive, high mortality could be due to higher loads of toxic compounds or the presence of chlorophyllous tissue.
My life with pulmonary arterial hypertension: a patient perspective
Authors: Ferrari Pisana , Skåra Hall 
Published: December 2019

AbstractIn recent years, there has been an increase in therapeutic options and treatment strategies for pulmonary arterial hypertension (PAH). However, patients still report delays in receiving a diagnosis, which is a significant burden associated with the disease, and which shows a general lack of disease awareness. This review has been written by two PAH patients to describe the patient experience and explore the ways in which patients are increasingly being given a voice in developing approaches to treatment. As patients with PAH are living longer, it is important that they work with healthcare professionals to develop treatment strategies that improve and maintain quality of life. Healthcare professionals should consider a holistic approach to disease management, including dietary recommendations, individually adapted exercise, and options for counselling where available, alongside therapeutic treatments. The experiences of patients with PAH are important not just for individual patient treatment but should also be considered in clinical trial design and guideline development. Patient representatives and patient associations can play an influential role in improving the treatment and management of PAH. In this review, we use our experiences as patient representatives to describe the current situation of patients with PAH from first experiencing symptoms to receiving treatment, using two patient cases as examples. We also discuss the role of patient advocacy in improving PAH care and future roles for patient associations and patient representatives in the design of clinical trials and development of new treatment guidelines.
Error reporting and the performance of nursing management: a game-theoretic study
Authors: Barrachina Alex , González-Chordá Víctor M 
Published: December 2019

AbstractThe interaction between nurses and their managers is a very important factor in nurses’ error reporting behaviour, which is crucial to improving patient safety in healthcare organizations. However, little theoretical work has been undertaken to analyse this interaction. This paper uses a game-theoretic principal–agent framework with asymmetric information to study this interaction. We suppose that the principal (the nurse manager) asks the agent (the nurse) to perform a task with a certain patient. In case a mistake is made while treating the patient, the nurse has to decide whether to report it to the manager, who can observe whether the patient suffered an accident. We consider different manager’s leadership styles and analyse their performance in obtaining error notification from nurses in this framework.
Jeu de taquin, uniqueness of rectification and ultradiscrete KP
Authors: Iwao Shinsuke 
Published: December 2019

Abstract
In this article, we study tropical-theoretic aspects of the ‘rectification algorithm’ on skew Young tableaux. It is shown that the algorithm is interpreted as a time evolution of some tropical integrable system. By using this fact, we construct a new combinatorial map that is essentially equivalent to the rectification algorithm. Some of properties of the rectification can be seen more clearly via this map. For example, the uniqueness of a rectification boils down to an easy combinatorial problem. Our method is mainly based on the two previous researches: the theory of geometric tableaux by Noumi–Yamada, and the study on the relationship between jeu de taquin slides and the ultradiscrete KP equation by Mikami and Katayama–Kakei.
When States Crack Down on Human Rights Defenders
Authors: Bakke Kristin M , Mitchell Neil J , Smidt Hannah M 
Published: December 2019

Abstract
Research suggests that civil society mobilization together with the ratification of human rights treaties put pressure on governments to improve their human rights practices. An unexplored theoretical implication is that pressure provokes counterpressure. Instead of improving treaty compliance, some governments will have an interest in demobilizing civil society to silence their critics. Yet we do not know how and to what extent this incentive shapes governments’ policies and practices regarding civil society organizations. In this article we argue and show—using a new global database of government-sponsored restrictions on civil society organizations—that when governments have committed to human rights treaties and, at the same time, continue to commit severe human rights abuses, they impose restrictions on civil society groups to avoid monitoring and mitigate the international costs of abuses.
Comparison of 2 fixatives in the porcine colon for in situ microbiota studies
Authors: Blick Anna K , Giaretta Paula R , Sprayberry Sarah , Bush-Vadala Clara , Paulk Chad B , Boeckman Justin , Callaway Todd R , Gill Jason J , Rech Raquel R 
Published: December 2019

AbstractFixation is the first step towards preservation of tissues and can impact downstream histological applications. Historically, formalin has been the fixative of choice in both research and clinical settings due to cost, accessibility, and broad applicability. Here, we describe a method for collection of porcine colon, and compare the usage of Carnoy’s solution (CS) to a 10% neutral buffered formalin (NBF) in tissue fixation. Consecutive colon samples were collected from 24 four-wk-old piglets and fixed in CS for 45 min or NBF for 24 h. We measured the thickness of the inner mucus layer using Alcian Blue stain and found thicker inner mucus layers in porcine colons fixed with CS as compared to NBF (P &lt; 0.0001). Carnoy’s solution-fixed colon exhibited greater bacterial cell counts than NBF-fixed colon (P &lt; 0.0022) after labeling with an eubacterial probe in fluorescent in situ hybridization (FISH). No difference was observed between the mucosal height (P = 0.42) and number of goblet cells (P = 0.66) between the 2 fixatives. From this, we concluded CS is more suitable than NBF for the preservation of the mucus layer and the associated mucosal bacteria in the porcine colon without compromising on overall tissue morphology. This study provides a useful sampling and fixation methodology for histology studies in the porcine gastrointestinal tract, and may be beneficial to microbiota, pathology, and nutrition studies.
Playing the Spinal Chord: Tantric Musicology and Bengali Songs in the Nineteenth Century
Authors: Williams Richard David 
Published: December 2019

AbstractAcross the nineteenth century, Bengali songbook editors applied musicological theory to their tantric religious practices. Responding to the new possibilities of musical publishing, these editors developed innovative techniques of relating the body to music by tying together tantric tropes with music theory and performance practice. Theories about the affective potential and poetic connotations of rāgas were brought into conversation with understandings of the yogic body, cakras, and the visualization of goddesses. These different theories, stemming from aesthetics and yogic philosophy, were put into effect through lyrical composition and the ways in which songs were set to music and edited for printed anthologies. This article considers different examples of tantric musical editorial, and explores how esoteric knowledge was applied in innovative ways through the medium of printed musical literature.
The importance of mesorectum motion in determining PTV margins in rectal cancer patients treated with neoadjuvant radiotherapy
Authors: Alickikus Zumre Arican , Kuru Ahmet , Aydin Barbaros , Akcay Dogukan , Gorken Ilknur Bilkay 
Published: December 2019

Abstract
New precision radiotherapy (RT) techniques reduce the uncertainties in localizing soft and moving tumors. However, there are still many uncontrollable internal organ movements. In our study, patients who underwent neoadjuvant chemoradiotherapy (NA-CRT) for rectal cancer were evaluated to determine inter-fraction mesorectum motion and dosimetric changes. Fourteen patients treated with NA-CRT for rectal cancer between 2014 and 2016 were included in the analysis. The mesorectum and clinical target volume (CTV) were delineated on planning computed tomography (CT) and cone-beam CT (CB-CT) scans. After planning with a volumetric modulated arc therapy (VMAT) plan, re-planning was performed on all CB-CTs. Finally, the volumetric and dosimetric changes of PTV and mesorectum were evaluated in all CB-CTs compared with the initial CT and VMAT plans. The geometrical center of mesorectum volume in CB-CTs had moved 1 (0.2–6.6), 1.6 (0.2–3.8) and 1.6 (0–4.9) mm in the x, y and z-axis respectively compared with the initial CT. The dosimetric parameters of PTV including D2, D95 and D98 on CB-CT showed a median 47.19 (46.70–47.80), 45.05 (44.18–45.68) and 44.69 (43.83–45.48) Gy and median 1% (1–2), 0% (0–2) and 1% (0–2) dosimetric change compared with the initial VMAT plan. In our study, we have shown that the mesorectum has moved up to 20 mm in the lateral and anterior–posterior direction and almost 10 mm in the superior/inferior direction during RT, causing a median of ~2% change in dosimetric parameters. Therefore, these movements must be considered in determining PTV margins to avoid dosimetric changes.
Measurement of Social Integration: Syrian Women in Turkey
Authors: Açikalin Şuay Nilhan , Erçetin Şefika Şule , Potas Nihan , Çevik M. Sabir , Neyişçi Nilay Başar , Görgülü Deniz 
Published: December 2019

Abstract
The concept of integration, defined as a harmonization process between the host society and immigrants, aims to maintain peaceful and social relationships. This study aims to measure the social integration of immigrants; to analyse multidimensionality the integration level of women Syrian refugees in Turkey; and to determine whether the integration status of refugee women differs according to age, marital status, number of children in the family and number of individuals in the family. In the study, the Social Integration of Immigrant Scale, which consists of four sub-dimensions, was used as a data-collection tool. When the validity and reliability analysis results of the scale were evaluated, it was concluded that Social Integration of Immigrant Scale was an appropriate instrument for psychometric use. In the result of the research, it was seen that refugee women have a high level of integration. It has been concluded that the social integration of Syrian women is highest in education and lowest in social inclusion.
Dualism or Paradox? A New ‘Light’ on the Gospel of John
Authors: Estes Douglas 
Published: December 2019

Abstract
Modern scholarship maintains the Gospel of John is dualistic. This view is uneasily held as there is a growing move to distance the gospel from the original history-of-religions concept of dualism that reached its peak in the mid-twentieth century with expectations of incipient Gnosticism in John. Instead of further nuancing the dualistic-sounding ideas in John, this essay challenges directly the claim that John is dualistic—and it proposes that what is often understood to be a dualistic metaphysic is actually paradoxical language as part of the Gospel’s oral and literary language games. Starting with a survey of how dualism entered into the scholarly purview of John, the essay then turns to the meaning and function of paradox in the ancient world. Since scholars point to John’s ‘light’ and ‘darkness’ imagery as the most prominent example of dualism, this essay uses the paradox language of ‘light’ and ‘darkness’ as a test case to demonstrate how paradox, and not dualism, is a more accurate and historical descriptor for John’s communicative strategy.
Capture of interstellar objects: a source of long-period comets
Authors: Hands T O , Dehnen W 
Published: December 2019

ABSTRACT
We simulate the passage through the Sun–Jupiter system of interstellar objects (ISOs) similar to 1I/‘Oumuamua or 2I/Borisov. Capture of such objects is rare and overwhelmingly from low incoming speeds on to orbits akin to those of known long-period comets. This suggests that some of these comets could be of extrasolar origin, in particular inactive ones. Assuming ISOs follow the local stellar velocity distribution, we infer a volume capture rate of $0.051\, \mathrm{au}^3\, \mathrm{yr}^{-1}$. Current estimates for orbital lifetimes and space densities then imply steady-state captured populations of ∼102 comets and ∼105 ‘Oumuamua-like rocks, of which 0.033 per cent are within 6 au at any time.