bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic summarisation: 25 years On
Authors: Orăsan Constantin 
Published: September 2019

AbstractAutomatic text summarisation is a topic that has been receiving attention from the research community from the early days of computational linguistics, but it really took off around 25 years ago. This article presents the main developments from the last 25 years. It starts by defining what a summary is and how its definition changed over time as a result of the interest in processing new types of documents. The article continues with a brief history of the field and highlights the main challenges posed by the evaluation of summaries. The article finishes with some thoughts about the future of the field.
Languages of Law: Islamic Legal Cosmopolis and its Arabic and Malay Microcosmoi
Authors: KOORIA MAHMOOD 
Published: September 2019

AbstractIn premodern monsoon Asia, the legal worlds of major and minor traditions formed a cosmopolis of laws which expanded chronologically and geographically. Without necessarily replacing one another, they all coexisted in a larger domain with fluctuating influences over time and place. In this legal cosmopolis, each tradition had its own aggregation of diverse juridical, linguistic and contextual variants. In South and Southeast Asia, Islam has accordingly formed its own cosmopolis of law by incorporating a network of different juridical texts, institutions, jurists and scholars and by the meaningful use of these variants through shared vocabularies and languages. Focusing on the Shāfiʿī School of Islamic law and its major proponents in Malay and Arabic textual productions, this article argues that the intentional choice of alingua francacontributed to the wider reception and longer sustainability of this particular legal school. The Arabic and Malay microcosmoi thus strengthened the larger cosmopolis of Islamic law through transregional and translinguistic exchanges across legal, cultural and continental borders.
Cultural adaptation of cognitive behavioural therapy (CBT) for patients with depression and anxiety in Saudi Arabia and Bahrain: a qualitative study exploring views of patients, carers, and mental health professionals
Authors: Algahtani Haifa Mohammad Saleh , Almulhim Abdullah , AlNajjar Fatema Ali , Ali Mazen Khalil , Irfan Muhammad , Ayub Muhammad , Naeem Farooq 
Published: September 2019

AbstractWestern values influence cognitive behavioural therapy (CBT) as it was primarily developed and practised in the West. As understanding the cultural context has been linked to better therapy outcomes, it has been suggested that CBT might need modification to non-Western clients’ cultural backgrounds. Previously we developed a cost-effective approach to adapt CBT for clients in China and Pakistan. In this study, we applied the same methodology for local clients suffering from depression and anxiety in the Kingdom of Saudi Arabia and Bahrain. This study aimed to understand the views of patients with depression and anxiety, caregivers and mental health professionals about CBT to develop guidelines for culturally adapting CBT for depression and anxiety. We conducted semi-structured interviews with the patients (n= 42), caregivers (n= 11), and psychiatrists and psychologists (n= 16). The data were analysed using a thematic framework analysis by identifying emerging themes and categories. The themes emerging from the analyses of interviews by each interviewer were compared and contrasted with those of other interviewers. The results highlighted barriers of access to and strengths of CBT while working with these patient groups. Patients and their caregivers in both countries use a bio-psycho-spiritual-social model of illness and seek help from multiple sources. Therapists emphasized the need for using local idioms, culturally appropriate translation and minor adjustments in therapy. There were no thematic differences between the two sites. These findings will be used to culturally adapt a CBT manual, which will be tested in a randomized controlled trial.Key learning aimsAfter reading this article, readers will be able to:(1)Understand the need for cultural adaptation of CBT.(2)Identify the necessary steps to adapt CBT for the Muslim Arab population.(3)Understand the modifications required to deliver culturally adapted CBT for the Muslim Arab population.
The contribution of bullying victimisation to the burden of anxiety and depressive disorders in Australia
Authors: Jadambaa Amarzaya , Thomas Hannah J. , Scott James G. , Graves Nicholas , Brain David , Pacella Rosana 
Published: September 2019

Abstract

Aim
There is now a strong body of literature showing that bullying victimisation during childhood and adolescence precedes the later development of anxiety and depressive disorders. This study aimed to quantify the burden of anxiety and depressive disorders attributable to experiences of bullying victimisation for the Australian population.

Methods
This study updated a previous systematic review summarising the longitudinal association between bullying victimisation and anxiety and depressive disorders. Estimates from eligible studies published from inception until 18 August 2018 were included and meta-analyses were based on quality-effects models. Pooled relative risks were combined with a contemporary prevalence estimate for bullying victimisation for Australia in order to calculate population attributable fractions (PAFs) for the two mental disorder outcomes. PAFs were then applied to estimates of the burden of anxiety and depressive disorders in Australia expressed as disability-adjusted life years (DALYs).

Results
The findings from this study suggest 7.8% of the burden of anxiety disorders and 10.8% of the burden of depressive disorders are attributable to bullying victimisation in Australia. An estimated 30 656 DALYs or 0.52% (95% uncertainty interval 0.33–0.72%) of all DALYs in both sexes and all ages in Australia were attributable to experiences of bullying victimisation in childhood or adolescence.

Conclusion
There is convincing evidence to demonstrate a causal relationship between bullying victimisation and mental disorders. This study showed that bullying victimisation contributes a significant proportion of the burden of anxiety and depressive disorders. The investment and implementation of evidence-based intervention programmes that reduce bullying victimisation in schools could reduce the burden of disease arising from common mental disorders and improve the health of Australians.
Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Authors: Wang Li , Zhao Hongying , Li Jing , Xu Yingqi , Lan Yujia , Yin Wenkang , Liu Xiaoqin , Yu Lei , Lin Shihua , Du Michael Yifei , Li Xia , Xiao Yun , Zhang Yunpeng 
Published: September 2019

Abstract
Epigenetic modifications play critical roles in modulating gene expression, yet their roles in regulatory networks in human cell lines remain poorly characterized. We integrated multiomics data to construct directed regulatory networks with nodes and edges labeled with chromatin states in human cell lines. We observed extensive association of diverse chromatin states and network motifs. The gene expression analysis showed that diverse chromatin states of coherent type-1 feedforward loop (C1-FFL) and incoherent type-1 feedforward loops (I1-FFL) contributed to the dynamic expression patterns of targets. Notably, diverse chromatin state compositions could help C1- or I1-FFL to control a large number of distinct biological functions in human cell lines, such as four different types of chromatin state compositions cooperating with K562-associated C1-FFLs controlling “regulation of cytokinesis,” “G1/S transition of mitotic cell cycle,” “DNA recombination,” and “telomere maintenance,” respectively. Remarkably, we identified six chromatin state-marked C1-FFL instances (HCFC1-NFYA-ABL1, THAP1-USF1-BRCA2, ZNF263-USF1-UBA52, MYC-ATF1-UBA52, ELK1-EGR1-CCT4, and YY1-EGR1-INO80C) could act as prognostic biomarkers of acute myelogenous leukemia though influencing cancer-related biological functions, such as cell proliferation, telomere maintenance, and DNA recombination. Our results will provide novel insight for better understanding of chromatin state-mediated gene regulation and facilitate the identification of novel diagnostic and therapeutic biomarkers of human cancers.
Multicenter, randomised, open-label, non-comparative phase 2 trial on the efficacy and safety of the combination of bevacizumab and trabectedin with or without carboplatin in women with partially platinum-sensitive recurrent ovarian cancer
Authors: Colombo Nicoletta , Zaccarelli Eleonora , Baldoni Alessandra , Frezzini Simona , Scambia Giovanni , Palluzzi Eleonora , Tognon Germana , Lissoni Andrea A. , Rubino Daniela , Ferrero Annamaria , Farina Gabriella , Negri Emanuele , Pesenti Gritti Angela , Galli Francesca , Biagioli Elena , Rulli Eliana , Poli Davide , Gerardi Chiara , Torri Valter , Fossati Roldano , D‘Incalci Maurizio 
Published: September 2019

Abstract

Background
Trabectedin, in addition to its antiproliferative effect, can modify the tumour microenvironment and this could be synergistic with bevacizumab. The efficacy and safety of trabectedin and bevacizumab ± carboplatin have never been investigated.

Methods
In this phase 2 study, women progressing between 6 and 12 months since their last platinum-based therapy were randomised to Arm BT: bevacizumab, trabectedin every 21 days, or Arm BT+C: bevacizumab, trabectedin and carboplatin every 28 days, from cycles 1 to 6, then trabectedin and bevacizumab as in Arm BT. Primary endpoints were progression-free survival rate (PFS-6) and severe toxicity rate (ST-6) at 6 months, assuming a PFS-6 ≤35% for BT and ≤40% for BT+C as not of therapeutic interest and, for both arms, a ST-6  ≥ 30% as unacceptable.

Results
BT+C (21 patients) did not meet the safety criteria for the second stage (ST-6 45%; 95%CI: 23%–69%) but PFS-6 was 85% (95%CI: 62%–97%). BT (50 patients) had 75% PFS-6 (95%CI: 60%–87%) and 16% ST-6 (95%CI 7%–30%).

Conclusions
BT compared favourably with other platinum- and non-platinum-based regimens. The combination with carboplatin needs to be assessed further in a re-modulated safer schedule to confirm its apparent strong activity.

Clinical Trial Registration
NCT01735071 (Clinicaltrials.gov).
Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast
Authors: Ha So Dam , Ham Seokjin , Kim Min Young , Kim Ji Hyun , Jang Insoon , Lee Bo Bae , Lee Min Kyung , Hwang Jin-Taek , Roh Tae-Young , Kim TaeSoo 
Published: September 2019

AbstractIn yeast, Hda1 histone deacetylase complex (Hda1C) preferentially deacetylates histones H3 and H2B, and functionally interacts with Tup1 to repress transcription. However, previous studies identified global increases in histone H4 acetylation in cells lacking Hda1, a component of Hda1C. Here, we find that Hda1C binds to hyperactive genes, likely via the interaction between the Arb2 domain of Hda1 and RNA polymerase II. Additionally, we report that Hda1C specifically deacetylates H4, but not H3, at hyperactive genes to partially inhibit elongation. This role is contrast to that of the Set2–Rpd3S pathway deacetylating histones at infrequently transcribed genes. We also find that Hda1C deacetylates H3 at inactive genes to delay the kinetics of gene induction. Therefore, in addition to fine-tuning of transcriptional response via H3-specific deacetylation, Hda1C may modulate elongation by specifically deacetylating H4 at highly transcribed regions.
NPC1 regulates ER contacts with endocytic organelles to mediate cholesterol egress
Authors: Höglinger D. , Burgoyne T. , Sanchez-Heras E. , Hartwig P. , Colaco A. , Newton J. , Futter C. E. , Spiegel S. , Platt F. M. , Eden E. R 
Published: September 2019

AbstractTransport of dietary cholesterol from endocytic organelles to the endoplasmic reticulum (ER) is essential for cholesterol homoeostasis, but the mechanism and regulation of this transport remains poorly defined. Membrane contact sites (MCS), microdomains of close membrane apposition, are gaining attention as important platforms for non-vesicular, inter-organellar communication. Here we investigate the impact of ER-endocytic organelle MCS on cholesterol transport. We report a role for Niemann-Pick type C protein 1 (NPC1) in tethering ER-endocytic organelle MCS where it interacts with the ER-localised sterol transport protein Gramd1b to regulate cholesterol egress. We show that artificially tethering MCS rescues the cholesterol accumulation that characterises NPC1-deficient cells, consistent with direct lysosome to ER cholesterol transport across MCS. Finally, we identify an expanded population of lysosome-mitochondria MCS in cells depleted of NPC1 or Gramd1b that is dependent on the late endosomal sterol-binding protein STARD3, likely underlying the mitochondrial cholesterol accumulation in NPC1-deficient cells.
Development of a longevous two-species biophotovoltaics with constrained electron flow
Authors: Zhu Huawei , Meng Hengkai , Zhang Wei , Gao Haichun , Zhou Jie , Zhang Yanping , Li Yin 
Published: September 2019

AbstractMicrobial biophotovoltaics (BPV) offers a biological solution for renewable energy production by using photosynthetic microorganisms as light absorbers. Although abiotic engineering approaches, e.g., electrode modification and device optimization, can enhance the electrochemical communication between living cells and electrodes, the power densities of BPV are still low due to the weak exoelectrogenic activity of photosynthetic microorganisms. Here, we develop a BPV based on ad-lactate mediated microbial consortium consisting of photosynthetic cyanobacteria and exoelectrogenicShewanella. By directing solar energy from photons tod-lactate, then to electricity, this BPV generates a power density of over 150 mW·m−2in a temporal separation setup. Furthermore, a spatial-temporal separation setup with medium replenishment enables stable operation for over 40 days with an average power density of 135 mW·m−2. These results demonstrate the electron flow constrained microbial consortium can facilitate electron export from photosynthetic cells and achieve an efficient and durable power output.
Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals
Authors: Gentsch George E. , Spruce Thomas , Owens Nick D. L. , Smith James C. 
Published: September 2019

AbstractEmbryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
Plasticity in striatal dopamine release is governed by release-independent depression and the dopamine transporter
Authors: Condon Mark D. , Platt Nicola J. , Zhang Yan-Feng , Roberts Bradley M. , Clements Michael A. , Vietti-Michelina Stefania , Tseu Min-Yee , Brimblecombe Katherine R. , Threlfell Sarah , Mann Edward O. , Cragg Stephanie J. 
Published: September 2019

AbstractMesostriatal dopaminergic neurons possess extensively branched axonal arbours. Whether action potentials are converted to dopamine output in the striatum will be influenced dynamically and critically by axonal properties and mechanisms that are poorly understood. Here, we address the roles for mechanisms governing release probability and axonal activity in determining short‐term plasticity of dopamine release, using fast‐scan cyclic voltammetry in the ex vivo mouse striatum. We show that brief short‐term facilitation and longer short term depression are only weakly dependent on the level of initial release, i.e. are release insensitive. Rather, short-term plasticity is strongly determined by mechanisms which govern axonal activation, including K+‐gated excitability and the dopamine transporter, particularly in the dorsal striatum. We identify the dopamine transporter as a master regulator of dopamine short‐term plasticity, governing the balance between release‐dependent and independent mechanisms that also show region‐specific gating.
Characterisation and localisation of the endocannabinoid system components in the adult human testis
Authors: Nielsen John E. , Rolland Antoine D. , Rajpert-De Meyts Ewa , Janfelt Christian , Jørgensen Anne , Winge Sofia B. , Kristensen David M. , Juul Anders , Chalmel Frédéric , Jégou Bernard , Skakkebaek Niels E. 
Published: September 2019

AbstractHeavy use of cannabis (marijuana) has been associated with decreased semen quality, which may reflect disruption of the endocannabinoid system (ECS) in the male reproductive tract by exogenous cannabinoids. Components of ECS have been previously described in human spermatozoa and in the rodent testis but there is little information on the ECS expression within the human testis. In this study we characterised the main components of the ECS by immunohistochemistry (IHC) on archived testis tissue samples from 15 patients, and by in silico analysis of existing transcriptome datasets from testicular cell populations. The presence of 2-arachidonoylglycerol (2-AG) in the human testis was confirmed by matrix-assisted laser desorption ionization imaging analysis. Endocannabinoid-synthesising enzymes; diacylglycerol lipase (DAGL) and N-acyl-phosphatidylethanolamine-specific phospholipase D (NAPE-PLD), were detected in germ cells and somatic cells, respectively. The cannabinoid receptors, CNR1 and CNR2 were detected at a low level in post-meiotic germ cells and Leydig- and peritubular cells. Different transcripts encoding distinct receptor isoforms (CB1, CB1A, CB1B and CB2A) were also differentially distributed, mainly in germ cells. The cannabinoid-metabolising enzymes were abundantly present; the α/β-hydrolase domain-containing protein 2 (ABHD2) in all germ cell types, except early spermatocytes, the monoacylglycerol lipase (MGLL) in Sertoli cells, and the fatty acid amide hydrolase (FAAH) in late spermatocytes and post-meiotic germ cells. Our findings are consistent with a direct involvement of the ECS in regulation of human testicular physiology, including spermatogenesis and Leydig cell function. The study provides new evidence supporting observations that recreational cannabis can have possible deleterious effects on human testicular function.
Microarray-based screening system identifies temperature-controlled activity of Connexin 26 that is distorted by mutations
Authors: Wang Hongling , Stahl Frank , Scheper Thomas , Steffens Melanie , Warnecke Athanasia , Zeilinger Carsten 
Published: September 2019

AbstractHere, we show that human Connexin 26 (hCx26 or Cx26WT) hemichannel opening rapidly enables the transport of small molecules when triggered by temperature and by compensation of the Ca2+ blockade with EDTA. Point mutations within Cx26 were analysed by a novel optical microarray-based Lucifer Yellow uptake assay or by two electrode voltage clamp (TEVC) on frog oocytes to monitor simultaneous activities of channel proteins. Point mutations L90P, F161S, R184P or K188N influenced the temperature-dependent activity drastically. Since several mutations blocked trafficking, the temperature-dependent activity of the recombinant synthesized and purified wild-type Cx26WT and Cx26K188N hemichannel was tested by liposome flux assay (LFA) and on a microarray-based Lucifer Yellow uptake assay under warm conditions (>30 °C). The data from TEVC measurements and dye flux experiments showed that the mutations gave no or only a weak activity at increased temperature (>30 °C). We conclude that the position K188 in the Cx26WT forms a temperature-sensitive salt bridge with E47 whereas the exchange to K188N destabilizes the network loop- gating filter, which was recently identified as a part of the flexible Ca2+ binding site. We assume that the temperature sensitivity of Cx26 is required to protect cells from uncontrolled release or uptake activities through Cx26 hemichannels.
Mid- to long-wave infrared computational spectroscopy using a subwavelength coaxial aperture array
Authors: Craig Benjamin J. , Meng Jiajun , Shrestha Vivek Raj , Cadusch Jasper J. , Crozier Kenneth B. 
Published: September 2019

AbstractMiniaturized spectrometers are advantageous for many applications and can be achieved by what we term the filter-array detector-array (FADA) approach. In this method, each element of an optical filter array filters the light that is transmitted to the matching element of a photodetector array. By providing the outputs of the photodetector array and the filter transmission functions to a reconstruction algorithm, the spectrum of the light illuminating the FADA device can be estimated. Here, we experimentally demonstrate an array of 101 band-pass transmission filters that span the mid- to long-wave infrared (6.2 to 14.2 μm). Each filter comprises a sub-wavelength array of coaxial apertures in a gold film. As a proof-of-principle demonstration of the FADA approach, we use a Fourier transform infrared (FTIR) microscope to record the optical power transmitted through each filter. We provide this information, along with the transmission spectra of the filters, to a recursive least squares (RLS) algorithm that estimates the incident spectrum. We reconstruct the spectrum of the infrared light source of our FTIR and the transmission spectra of three polymer-type materials: polyethylene, cellophane and polyvinyl chloride. Reconstructed spectra are in very good agreement with those obtained via direct measurement by our FTIR system.
The ERC1 scaffold protein implicated in cell motility drives the assembly of a liquid phase
Authors: Sala Kristyna , Corbetta Agnese , Minici Claudia , Tonoli Diletta , Murray David H. , Cammarota Eugenia , Ribolla Lucrezia , Ramella Martina , Fesce Riccardo , Mazza Davide , Degano Massimo , de Curtis Ivan 
Published: September 2019

AbstractSeveral cellular processes depend on networks of proteins assembled at specific sites near the plasma membrane. Scaffold proteins assemble these networks by recruiting relevant molecules. The scaffold protein ERC1/ELKS and its partners promote cell migration and invasion, and assemble into dynamic networks at the protruding edge of cells. Here by electron microscopy and single molecule analysis we identify ERC1 as an extended flexible dimer. We found that ERC1 scaffolds form cytoplasmic condensates with a behavior that is consistent with liquid phases that are modulated by a predicted disordered region of ERC1. These condensates specifically host partners of a network relevant to cell motility, including liprin-α1, which was unnecessary for the formation of condensates, but influenced their dynamic behavior. Phase separation at specific sites of the cell periphery may represent an elegant mechanism to control the assembly and turnover of dynamic scaffolds needed for the spatial localization and processing of molecules.