bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding all maximal perfect haplotype blocks in linear time
Authors: Alanko Jarno , Bannai Hideo , Cazaux Bastien , Peterlongo Pierre , Stoye Jens 
Published: February 2020

AbstractRecent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals’ haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Advances in bioinformatics and computational biology: 11th Brazilian symposium on bioinformatics, BSB 2018, Niterói, Brazil, October 30 - November 1, 2018, Proceedings, 2018. 10.1007/978-3-030-01722-4_3) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows–Wheeler Transform, that is very efficient also in practice.
Five new cases of syndromic intellectual disability due to KAT6A mutations: widening the molecular and clinical spectrum
Authors: Urreizti Roser , Lopez-Martin Estrella , Martinez-Monseny Antonio , Pujadas Montse , Castilla-Vallmanya Laura , Pérez-Jurado Luis Alberto , Serrano Mercedes , Natera-de Benito Daniel , Martínez-Delgado Beatriz , Posada-de-la-Paz Manuel , Alonso Javier , Marin-Reina Purificación , O’Callaghan Mar , Grinberg Daniel , Bermejo-Sánchez Eva , Balcells Susanna 
Published: February 2020

Abstract
Background
Pathogenic variants of the lysine acetyltransferase 6A or KAT6A gene are associated with a newly identified neurodevelopmental disorder characterized mainly by intellectual disability of variable severity and speech delay, hypotonia, and heart and eye malformations. Although loss of function (LoF) mutations were initially reported as causing this disorder, missense mutations, to date always involving serine residues, have recently been associated with a form of the disorder without cardiac involvement.

Results
In this study we present five new patients, four with truncating mutations and one with a missense change and the only one not presenting with cardiac anomalies. The missense change [p.(Gly359Ser)], also predicted to affect splicing by in silico tools, was functionally tested in the patient’s lymphocyte RNA revealing a splicing effect for this allele that would lead to a frameshift and premature truncation.

Conclusions
An extensive revision of the clinical features of these five patients revealed high concordance with the 80 cases previously reported, including developmental delay with speech delay, feeding difficulties, hypotonia, a high bulbous nose, and recurrent infections. Other features present in some of these five patients, such as cryptorchidism in males, syndactyly, and trigonocephaly, expand the clinical spectrum of this syndrome.
2DKD: a toolkit for content-based local image search
Authors: DeVille Julian S. , Kihara Daisuke , Sit Atilla 
Published: February 2020

Abstract
Background
Direct comparison of 2D images is computationally inefficient due to the need for translation, rotation, and scaling of the images to evaluate their similarity. In many biological applications, such as digital pathology and cryo-EM, often identifying specific local regions of images is of particular interest. Therefore, finding invariant descriptors that can efficiently retrieve local image patches or subimages becomes necessary.

Results
We present a software package called Two-Dimensional Krawtchouk Descriptors that allows to perform local subimage search in 2D images. The new toolkit uses only a small number of invariant descriptors per image for efficient local image retrieval. This enables querying an image and comparing similar patterns locally across a potentially large database. We show that these descriptors appear to be useful for searching local patterns or small particles in images and demonstrate some test cases that can be helpful for both assembly software developers and their users.

Conclusions
Local image comparison and subimage search can prove cumbersome in both computational complexity and runtime, due to factors such as the rotation, scaling, and translation of the object in question. By using the 2DKD toolkit, relatively few descriptors are developed to describe a given image, and this can be achieved with minimal memory usage.
Evaluation of a new set of indicators for mental health care implemented in Madhya Pradesh, India: a mixed methods study
Authors: Ahuja Shalini , Khan Azaz , Goulding Lucy , Bansal Rachel Kaur , Shidhaye Rahul , Thornicroft Graham , Jordans Mark 
Published: February 2020

Abstract
Background
Mental health information systems are, in general, inadequate and unreliable in India. We have developed key mental health indicators for measuring mental health service coverage in primary care. This study aims to evaluate the use of these new indicators in seven health care facilities in Sehore District of Madhya Pradesh in India.

Methods
The study employed a mixed methods approach. We conducted: a qualitative study (n = 26) with health workers, Health Management Information Systems (HMIS) staff, project coordinators and supervisors; a review of case records (n = 61 at time 1 and n = 74 at time 2); and a structured questionnaire (n = 26) with health workers. The performance, user-friendliness, appropriateness, perceived utility and sustainability of the use of new mental health indicators was assessed.

Results
High levels of completion, and correctness of completion, of the new mental health indicators were found for the case records. The simplicity of the forms, as well as technical support from the project team, contributed to acceptability and feasibility of implementation. Perceived sustainability of the new forms was, however, affected by the overstretched primary care staff. Further work is needed to support the integration of mental health with routine HMIS.

Conclusion
This study demonstrated that the implementation of key mental health service delivery indicators in Sehore District primary care facilities was feasible. Technical assistance was imperative in maintaining the performance of the indicators over the two studied time points. The integration of mental health indicators in routine health information systems, and political buy-in, are needed to monitor and sustain community mental health programmes in India.
Impact of a paediatric-adult care transition programme on the health status of patients with sickle cell disease: study protocol for a randomised controlled trial (the DREPADO trial)
Authors:   DREPADO study group, Hoegy Delphine , Bleyzac Nathalie , Gauthier-Vasserot Alexandra , Cannas Giovanna , Denis Angélique , Hot Arnaud , Bertrand Yves , Occelli Pauline , Touzet Sandrine , Dussart Claude , Janoly-Dumenil Audrey 
Published: February 2020

Abstract
Background
Thanks to advancements in medical care, a majority of patients with sickle cell disease (SCD) worldwide live beyond 18 years of age, and therefore, patients initially followed in paediatric departments are then transferred to adult departments. This paediatric-adult care transition is a period with an increased risk of discontinuity of care and subsequent morbidity and mortality. During this period, the patient will have to manage new interlocutors and places of care, and personal issues related to the period of adolescence. To take into consideration all these aspects, an interesting approach is to use the whole system approach to the patient, as presented in the biopsychosocial approach. The aim of this trial is to evaluate the impact of the proposed biopsychosocial paediatric-adult transition programme.

Methods
The DREPADO study is a multicentre randomised control trial comparing a control group (Arm A) to an interventional group with a paediatric-adult transition programme based on a biopsychosocial approach (Arm B). To be included, patients should have the SS, SC, or Sβ form of sickle cell disease and be aged between 16 and 17 years. The randomisation in a 1:1 ratio assigns to Arm A or B. The primary outcome is the number of hospital admissions and emergencies for complications in the index hospital, in the 2 years after the first consultation in the adult department of care. Secondary outcomes consider the quality of life, but also include coping skills such as sense of self-efficacy and disease knowledge. To provide patient and parent knowledge and coping skills, the transition programme is composed of three axes: educational, psychological, and social, conducted individually and in groups.

Discussion
By providing self-care knowledge and coping skills related to SCD and therapeutics, helping empower patientsin relation to pain management and emotions, and facilitating the relationship to oneself, others, and care in Arm B of the DREPADO study, we believe that the morbidity and mortality of patients with SCD may be reduced after the proposed paediatric-adult transition programme.

Trial registration
ClinicalTrials.gov, ID: NCT03786549; registered on 17 December 2018; https://clinicaltrials.gov/.
Potential of selected lactic acid bacteria from Theobroma cacao fermented fruit juice and cell-free supernatants from cultures as inhibitors of Helicobacter pylori and as good probiotic
Authors: Kouitcheu Mabeku Laure Brigitte , Ngue Samuel , Bonsou Nguemo Idris , Leundji Hubert 
Published: February 2020

Abstract
Objective
The present study was designed to evaluate the inhibitory effect of lactic acid bacteria (LAB) isolates from the fermented cocoa juice and their cell-free culture supernatants (CFS) against Helicobacter pylori strains and their potential as good probiotic. Isolation of lactic acid bacteria (LAB) was performed by culture and subculture of sample on MRS agar. Morphological characteristics, Gram staining and catalase reaction were used to identify the isolates. The antagonistic activity of LAB was tested using the agar spot-on-lawn method and the inhibitory effect of CFS using well diffusion assay. Acid tolerance and resistance to antibiotics tests were used to evaluate the probiotic potential of LAB isolates.

Results
Antagonistic effect was observed in 65.52% of isolated LAB. Isolate LAB19 showed the broader spectrum of antagonistic effect. The overall inhibitory activity was two to three folds reduced when CFSs were used instead of LAB isolates themselves. Our data showed that LAB19 controlled H. pylori growth using bacteriocins and that LAB4′, LAB8, LAB11′, LAB12, LAB13′, LAB15, LAB16 and LAB17 were through organic acids. LAB9, LAB11′ and LAB12 showed properties of probiotic tested. In this study, nine LAB isolates were found to possess anti-Helicobacter activity and some preliminary probiotic properties.
Physicochemical quality of water and health risks associated with consumption of African lung fish (Protopterus annectens) from Nyabarongo and Nyabugogo rivers, Rwanda
Authors: Omara Timothy , Nteziyaremye Papias , Akaganyira Solomon , Opio Dickens Waswa , Karanja Lucy Nyambura , Nyangena Decrah Moraa , Kiptui Betty Jematia , Ogwang Remish , Epiaka Stephen Mark , Jepchirchir Abigael , Maiyo Alfayo 
Published: February 2020

Abstract
Objective
To determine the quality of water, heavy metal content of edible muscles of a piscivorous fish (Protopterus annectens) and assess the health risks associated with using water and consumption of P. annectens from Nyabarongo and Nyabugogo rivers of Rwanda.

Results
All the water quality parameters were within World Health Organization’s acceptable limits except total nitrogen, iron, manganese and lead levels. Edible muscles of Protopterus annectens contained 272.8 ± 0.36, 292.2 ± 0.25, 8.8 ± 0.36, 135.2 ± 0.15, 148.0 ± 0.21 and 432. 0 ± 0.50 mg/kg of iron, manganese, copper, zinc, chromium and lead at Ruliba station and 336.0 ± 0.70, 302.6 ± 1.22, 6.4 ± 0.26, 44.7 ± 0.20, 138.2 ± 0.17 and 302.4 ± 1.50 mg/kg of iron, manganese, copper, zinc, chromium and lead at Kirinda bridge of Nyabarongo river. Health risk assessments indicated that though ingestion and dermal contact with heavy metals in water from the rivers may not cause obvious health effects, consumption of Protopterus annectens from Nyabarongo river may lead to deleterious health effects.
Binaural sound localization based on deep neural network and affinity propagation clustering in mismatched HRTF condition
Authors: Wang Jing , Wang Jin , Qian Kai , Xie Xiang , Kuang Jingming 
Published: February 2020

AbstractBinaural sound source localization is an important and widely used perceptually based method and it has been applied to machine learning studies by many researchers based on head-related transfer function (HRTF). Because the HRTF is closely related to human physiological structure, the HRTFs vary between individuals. Related machine learning studies to date tend to focus on binaural localization in reverberant or noisy environments, or in conditions with multiple simultaneously active sound sources. In contrast, mismatched HRTF condition, in which the HRTFs used to generate the training and test sets are different, is rarely studied. This mismatch leads to a degradation of localization performance. A basic solution to this problem is to introduce more data to improve generalization performance, which requires a lot. However, simply increasing the data volume will result in data-inefficiency. In this paper, we propose a data-efficient method based on deep neural network (DNN) and clustering to improve binaural localization performance in the mismatched HRTF condition. Firstly, we analyze the relationship between binaural cues and the sound source localization with a classification DNN. Different HRTFs are used to generate training and test sets, respectively. On this basis, we study the localization performance of DNN model trained by each training set on different test sets. The result shows that the localization performance of the same model on different test sets is different, while the localization performance of different models on the same test set may be similar. The result also shows a clustering trend. Secondly, different HRTFs are divided into several clusters. Finally, the corresponding HRTFs of each cluster center are selected to generate a new training set and to train a more generalized DNN model. The experimental results show that the proposed method achieves better generalization performance than the baseline methods in the mismatched HRTF condition and has almost equal performance to the DNN trained with a large number of HRTFs, which means the proposed method is data-efficient.
Thunderstorm identification algorithm research based on simulated airborne weather radar reflectivity data
Authors: Wang Xu , Liao Rui , Li Jing , He Jianxin , Wang Guoqiang , Xu Zili , Wang Haijiang 
Published: February 2020

AbstractIn the past few decades, radar reflectivity data have been widely used in thunderstorm identification research. Many thunderstorm identification algorithms for ground-based weather radar have been developed. But for airborne weather radar, due to the relative scarcity of data, the thunderstorm identification research is insufficient and there are still few effective identification methods. Airborne weather radar has the realization capability of close-range detection, but most existing airborne weather radars do not have scanning capability. This paper proposes an airborne weather radar volume scan mode, under which there is a total of 31 sector scans at 31 elevations in a volume scan. And a reflectivity data simulation model of the airborne weather radar is established based on this scan strategy, then the ground-based X-band radar reflectivity data are used as input to obtain the simulated X-band airborne radar reflectivity data. Moreover, this paper studies a thunderstorm identification algorithm for the X-band airborne radar with the proposed scan mode. An improved SCI (storm cell identification) algorithm is proposed on the basis of the traditional SCI algorithm which is applicable to S-band ground-based weather radar. The results of thunderstorm identification carried out on the simulated airborne radar data show that the algorithm can effectively identify the thunderstorm cells in the mature stage and the developing stage.
Active acoustic telemetry tracking and tri-axial accelerometers reveal fine-scale movement strategies of a non-obligate ram ventilator
Authors: Meese Emily N. , Lowe Christopher G. 
Published: February 2020

AbstractBackgroundCalifornia horn sharks (Heterodontus francisci) are nocturnally active, non-obligate ram ventilating sharks in rocky reef habitats that play an important ecological role in regulating invertebrate communities. We predicted horn sharks would use an area restricted search (ARS) movement strategy to locate dense resource patches while minimizing energetic costs of travel and nighttime activity. As ectotherms, we predicted environmental temperature would play a significant role in driving movement and activity patterns.MethodsContinuous active acoustic tracking methods and acceleration data loggers were used to quantify the diel fine-scale spatial movements and activity patterns of horn sharks. First passage time was used to identify the scale and locations of patches indicative of ARS. Activity was assessed using overall dynamic body acceleration (ODBA) as a proxy for energy expenditure. Behavior within a patch was characterized into three activity patterns: resting, episodic burst activity, and moderate, consistent activity.ResultsAfter resting in daytime shelters, individuals travelled to multiple reefs throughout the night, traversing through depths of 2–112 m and temperatures of 10.0–23.8 °C. All sharks exhibited area restricted search patch use and arrived at their first patch approximately 3.4 ± 2.2 h (mean ± SD) after sunset. Sharks exhibited moderate, consistent activity in 54% of the patches used, episodic burst activity in 33%, and few (13%) were identified as resting at night. ODBA peaked while sharks were swimming through relatively deeper (~ 30 m), colder channels when traversing from one patch to the next. There was no consistent pattern between ODBA and temperature.ConclusionsWe provide one of the largest fine-scale, high-resolution paired data sets for an elasmobranch movement ecology study. Horn sharks exhibited ARS movement patterns for various activity patterns. Individuals likely travel to reefs known to have profitable and predictable patches, potentially tolerating less suitable environmental temperatures. We demonstrate how gathering high-resolution information on the movement decisions of a community resident enhances knowledge of community structure and overall ecosystem function.
Analysis and characterization of materials used in heritage theatrical figurines
Authors: Gong Yuxuan , Qiao Chengquan , Zhong Bochao , Zhong Jiarang , Gong Decai 
Published: February 2020

Abstract
The precious collections of the Qing Dynasty paper-made theatrical figurines known as Shage xiren (纱阁戏人) represent a unique type of Chinese traditional folk art. The name, “Shage xiren” can be explained as the theatrical figurines that display in gauze curtains covered showcases. There were originally 36 showcases of Shage xiren of which 34 are preserved with 28 showcases exhibited at Qingxu Taoist Temple of Pingyao and the other damaged 6 are kept in the storeroom. It is rare that ancient paper-made figurines can be retained; therefore Shage xiren became a valuable source for understanding the traditional folk art as well as exploring rarely inherited crafts. Due to the material specificity and the poor preservation conditions, most of the figurines are found with various damages. It appears necessary to carry out appropriate conservative and restorative actions. To date, very few works have been reported on investigating the materials and crafts of making Shage xiren, resulting in a lack of basis for restoration. In this research, the samples collected from the damaged figurines, including wooden stick, plant fibers, paper pieces, clay fragments and textile fibers were studied. Polarized light microscope, X-ray diffraction, granulometry, Raman spectrum, digital microscopy and Fourier transform infrared spectrum analyses were employed to characterize the materials used in producing the cultural relics. The results indicated that not only paper, but also various materials were utilized in making the figurines. To form well-shaped bodies, the figurines have moso bamboo sticks applied as supporting structures, then covered with wheat straw and filled with natural cotton. The paper costumes and decorations were made from coniferous wood pulp and bamboo fibers respectively, and the textile belts were made from silk. The heads, feet and fingers of the figurines were shaped with fine local clay mixed with natural fibers to prevent cracking. The heads were further applied with lime to improve the surface smoothness and brightness. The pigments of red lead, basic lead carbonate, indigo and artificial ultramarine were used in painting and dyeing the clay heads and feet, and paper decorations. Although the figurines were made from accessible materials, the ingenious design and the sophisticated skills combining sculpturing, paper folding and elaborate ornamenting made it one of the unique artefacts. This research further provided reliable evidence in guiding the conservation and restoration work.
Effects of heat treatment on the behavior of teak wood adherends bonded joints
Authors: Budhe S. , Banea M. D. , Ghugal S. , de Barros S. 
Published: February 2020

AbstractThe main aim of this work is to investigate the effect of heat treatment on the teak wood adherend bonded joints. Indian teak wood samples were kept in an oven at 150 °C for 2 h for the heat treatment process. The surface roughness values of the wood adherend before and after the heat treatment process were measured using a surface profilometer. Wettability of un-treated and heat-treated teak wood samples was determined with the contact angle measurements by using the sessile drop method. Single strap joints with un-treated and heat treated wood specimens were tested at ambient temperature. The results show that, there is a clear dependency observed in between the heat treatment and the surface roughness of the wood adherends. Wettability of teak wood adherend surface is degraded after the heat treatment process. An adverse effect of heat treatment of wood adherend on the bonding strength was observed, but the surface roughness was improved.