bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compression of Deep-Learning Models Through Global Weight Pruning Using Alternating Direction Method of Multipliers
Authors: Lee Kichun , Hwangbo Sunghun , Yang Dongwook , Lee Geonseok 
Published: February 2023

AbstractDeep learning has shown excellent performance in numerous machine-learning tasks, but one practical obstacle in deep learning is that the amount of computation and required memory is huge. Model compression, especially in deep learning, is very useful because it saves memory and reduces storage size while maintaining model performance. Model compression in a layered network structure aims to reduce the number of edges by pruning weights that are deemed unnecessary during the calculation. However, existing weight pruning methods perform a layer-by-layer reduction, which requires a predefined removal-ratio constraint for each layer. Layer-by-layer removal ratios must be structurally specified depending on the task, causing a sharp increase in the training time due to a large number of tuning parameters. Thus, such a layer-by-layer strategy is hardly feasible for deep layered models. Our proposed method aims to perform weight pruning in a deep layered network, while producing similar performance, by setting a global removal ratio for the entire model without prior knowledge of the structural characteristics. Our experiments with the proposed method show reliable and high-quality performance, obviating layer-by-layer removal ratios. Furthermore, experiments with increasing layers yield a pattern in the pruned weights that could provide an insight into the layers’ structural importance. The experiment with the LeNet-5 model using MNIST data results in a higher compression ratio of 98.8% for the proposed method, outperforming existing pruning algorithms. In the Resnet-56 experiment, the performance change according to removal ratios of 10–90% is investigated, and a higher removal ratio is achieved compared to other tested models. We also demonstrate the effectiveness of the proposed method with YOLOv4, a real-life object-detection model requiring substantial computation.
The DNA damage response in advanced ovarian cancer: functional analysis combined with machine learning identifies signatures that correlate with chemotherapy sensitivity and patient outcome
Authors: Walker Thomas D. J. , Faraahi Zahra F. , Price Marcus J. , Hawarden Amy , Waddell Caitlin A. , Russell Bryn , Jones Dominique M. , McCormick Aiste , Gavrielides N. , Tyagi S. , Woodhouse Laura C. , Whalley Bethany , Roberts Connor , Crosbie Emma J. , Edmondson Richard J. 
Published: February 2023

AbstractBackgroundOvarian cancers are hallmarked by chromosomal instability. New therapies deliver improved patient outcomes in relevant phenotypes, however therapy resistance and poor long-term survival signal requirements for better patient preselection. An impaired DNA damage response (DDR) is a major chemosensitivity determinant. Comprising five pathways, DDR redundancy is complex and rarely studied alongside chemoresistance influence from mitochondrial dysfunction. We developed functional assays to monitor DDR and mitochondrial states and trialled this suite on patient explants.MethodsWe profiled DDR and mitochondrial signatures in cultures from 16 primary-setting ovarian cancer patients receiving platinum chemotherapy. Explant signature relationships to patient progression-free (PFS) and overall survival (OS) were assessed by multiple statistical and machine-learning methods.ResultsDR dysregulation was wide-ranging. Defective HR (HRD) and NHEJ were near-mutually exclusive. HRD patients (44%) had increased SSB abrogation. HR competence was associated with perturbed mitochondria (78% vs 57% HRD) while every relapse patient harboured dysfunctional mitochondria. DDR signatures classified explant platinum cytotoxicity and mitochondrial dysregulation. Importantly, explant signatures classified patient PFS and OS.ConclusionsWhilst individual pathway scores are mechanistically insufficient to describe resistance, holistic DDR and mitochondrial states accurately predict patient survival. Our assay suite demonstrates promise for translational chemosensitivity prediction.
Selective inhibition of HDAC6 promotes bladder cancer radiosensitization and mitigates the radiation-induced CXCL1 signalling
Authors: Tsai Yu-Chieh , Wang Tzu-Yin , Hsu Chia-Lang , Lin Wei-Chou , Chen Jyun-Yu , Li Jia-Hua , Pu Yeong-Shiau , Cheng Ann-Lii , Cheng Jason Chia-Hsien , Su Sheng-Fang 
Published: February 2023

AbstractBackgroundAlthough trimodality therapy resecting tumours followed by chemoradiotherapy is emerged for muscle-invasive bladder cancer (MIBC), chemotherapy produces toxicities. Histone deacetylase inhibitors have been identified as an effective strategy to enhance cancer radiotherapy (RT).MethodsWe examined the role of HDAC6 and specific inhibition of HDAC6 on BC radiosensitivity by performing transcriptomic analysis and mechanism study.ResultsHDAC6 knockdown or HDAC6 inhibitor (HDAC6i) tubacin exerted a radiosensitizing effect, including decreased clonogenic survival, increased H3K9ac andα-tubulin acetylation, and accumulated γH2AX, which are similar to the effect of panobinostat, a pan-HDACi, on irradiated BC cells. Transcriptomics of shHDAC6-transduced T24 under irradiation showed that shHDAC6 counteracted RT-induced mRNA expression of CXCL1, SERPINE1, SDC1 and SDC2, which are linked to cell migration, angiogenesis and metastasis. Moreover, tubacin significantly suppressed RT-induced CXCL1 and radiation-enhanced invasion/migration, whereas panobinostat elevated RT-induced CXCL1 expression and invasion/migration abilities. This phenotype was significantly abrogated by anti-CXCL1 antibody, indicating the key regulator of CXCL1 contributing to BC malignancy. Immunohistochemical evaluation of tumours from urothelial carcinoma patients supported the correlation between high CXCL1 expression and reduced survival.ConclusionUnlike pan-HDACi, the selective HDAC6i can enhance BC radiosensitization and effectively inhibit RT-induced oncogenic CXCL1-Snail-signalling, thus further advancing its therapeutic potential with RT.
Alternative methods to measure breast density in younger women
Authors: Lloyd Rachel , Pirikahu Sarah , Walter Jane , Cadby Gemma , Darcey Ellie , Perera Dilukshi , Hickey Martha , Saunders Christobel , Karnowski Karol , Sampson David D. , Shepherd John , Lilge Lothar , Stone Jennifer 
Published: February 2023

Abstract
Background
Breast density is a strong and potentially modifiable breast cancer risk factor. Almost everything we know about breast density has been derived from mammography, and therefore, very little is known about breast density in younger women aged <40. This study examines the acceptability and performance of two alternative breast density measures, Optical Breast Spectroscopy (OBS) and Dual X-ray Absorptiometry (DXA), in women aged 18–40.

Methods
Breast tissue composition (percent water, collagen, and lipid content) was measured in 539 women aged 18–40 using OBS. For a subset of 169 women, breast density was also measured via DXA (percent fibroglandular dense volume (%FGV), absolute dense volume (FGV), and non-dense volume (NFGV)). Acceptability of the measurement procedures was assessed using an adapted validated questionnaire. Performance was assessed by examining the correlation and agreement between the measures and their associations with known determinants of mammographic breast density.

Results
Over 93% of participants deemed OBS and DXA to be acceptable. The correlation between OBS-%water + collagen and %FGV was 0.48. Age and BMI were inversely associated with OBS-%water + collagen and %FGV and positively associated with OBS-%lipid and NFGV.

Conclusions
OBS and DXA provide acceptable and viable alternative methods to measure breast density in younger women aged 18–40 years.
Sodium preintercalation-induced oxygen-deficient hydrated potassium manganese oxide for high-energy flexible Mg-ion supercapacitors
Authors: Liu Shude , Kang Ling , Zhang Jian , Jun Seong Chan , Yamauchi Yusuke 
Published: February 2023

AbstractLayered potassium manganese oxides are promising candidates for use in aqueous supercapacitors owing to their wide potential windows, layered feature, and Faradaic redox reactions that occur on surfaces and in bulk regions. However, the practical application is hindered by rapid performance degradation due to their inherently low electrical conductivities and inferior structural stabilities. Here, we develop ultralong nanobelts comprising hydrated Na-intercalated oxygen-deficient potassium manganese oxide (H-Na-D-KMO), in which the Na+ ions are preintercalated and synchronously induce the generation of oxygen vacancies, as high-energy-density and durable electrodes for Mg-ion supercapacitors. The experimental results indicated that preintercalation of Na+ ions and formation of oxygen vacancies improved the electrical properties and ion diffusion, which accounted for the fast reaction kinetics and good cycling performance of H-Na-D-KMO. The optimized H-Na-D-KMO delivered a significantly enhanced specific capacitance and cycling performance compared to those of pure H-KMO. Asymmetric supercapacitors with H-Na-D-KMO as the cathode and as-prepared MoO2@carbon as the anode exhibited an ultrahigh energy density of 108.4 Wh kg–1 at 11,000 Wh kg−1, which is superior to most supercapacitors reported in the literature. Moreover, the assembled device exhibited good cycling stability for over 5000 cycles with a fading rate of 0.002% per cycle and good mechanical flexibility, which opens an avenue for further advancements in high-energy supercapacitors.
Home-based screening tools for amblyopia: a systematic review
Authors: Sii Samantha Siaw Zhen , Chean Chung Shen , Kuht Helen , Bunce Catey , Thomas Mervyn G. , Rufai Sohaib R. 
Published: February 2023

AbstractAmblyopia is an important public health concern. While home-based screening may present an effective solution, this has not been rigorously assessed in a systematic review. A systematic review was performed using Ovid MEDLINE, PubMed, The Cochrane Library, Embase, Web of Science Core Collection, and Clinicaltrials.gov. All studies reporting the diagnostic accuracy of home-based screening tools for amblyopia among children were included. Studies involving orthoptist or ophthalmologist-led screening and adult subjects were excluded. The main outcome measure was the diagnostic accuracy expressed as sensitivity and specificity. Among 3670 studies identified, 28 were eligible for inclusion in our systematic review. The age range of patients were less than 1 month to 16 years old. 7 studies used internet-based tools, 16 used smartphone/tablet applications, 3 used digital cameras, and 3 used home-based questionnaires and visual acuity tools. All studies included a reference standard except one, which was a longitudinal study. 21 studies had full ophthalmological examination whilst 6 studies had validated visual acuity measurement tools as gold standards. Of the 27 studies which compared against a reference test, only 25 studies reported sensitivity and specificity values. Using the QUADAS-2 tool, 50% of studies were deemed to have applicability concern due to patient selection from tertiary centres and unclear methods for recruitment. There is a need to improve the quality of diagnostic accuracy studies, standardise thresholds for detecting amblyopia, and ensure consistent reporting of results. Further research is needed to evaluate the suitability of these tools for amblyopia screening.
Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes
Authors: Marasco Ramona , Fusi Marco , Coscolín Cristina , Barozzi Alan , Almendral David , Bargiela Rafael , Nutschel Christina Gohlke neé , Pfleger Christopher , Dittrich Jonas , Gohlke Holger , Matesanz Ruth , Sanchez-Carrillo Sergio , Mapelli Francesca , Chernikova Tatyana N. , Golyshin Peter N. , Ferrer Manuel , Daffonchio Daniele 
Published: February 2023

AbstractMicrobial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA
Authors: Davies Mark R. , Keller Nadia , Brouwer Stephan , Jespersen Magnus G. , Cork Amanda J. , Hayes Andrew J. , Pitt Miranda E. , De Oliveira David M. P. , Harbison-Price Nichaela , Bertolla Olivia M. , Mediati Daniel G. , Curren Bodie F. , Taiaroa George , Lacey Jake A. , Smith Helen V. , Fang Ning-Xia , Coin Lachlan J. M. , Stevens Kerrie , Tong Steven Y. C. , Sanderson-Smith Martina , Tree Jai J. , Irwin Adam D. , Grimwood Keith , Howden Benjamin P. , Jennison Amy V. , Walker Mark J. 
Published: February 2023

AbstractA new variant of Streptococcus pyogenes serotype M1 (designated ‘M1UK’) has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor S. pyogenes ‘M1global’ and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 S. pyogenes. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing S. pyogenes in Asia. A single SNP in the 5’ transcriptional leader sequence of the transfer-messenger RNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator read-through in the M1UK lineage. This represents a previously unappreciated mechanism of toxin expression and urges enhanced international surveillance.
PROCURE European consensus on breast cancer multigene signatures in early breast cancer management
Authors: Curigliano Giuseppe , Cardoso Fatima , Gnant Michael , Harbeck Nadia , King Judy , Laenkholm Anne-Vibeke , Penault-Llorca Frédérique , Prat Aleix 
Published: February 2023

AbstractBreast cancer multigene signatures (BCMS) have changed how patients with early-stage breast cancer (eBC) are managed, as they provide prognostic information and can be used to select patients who may avoid adjuvant chemotherapy. Clinical guidelines make recommendations on the use of BCMS; however, little is known on the current use of BCMS in clinical practice. We conduct a two-round Delphi survey to enquire about current use and perceived utility for specific patient profiles, and unmet needs of BCMS. Overall, 133 panellists experienced in breast cancer across 11 European countries have participated, most using BCMS either routinely (66.2%) or in selected cases (27.1%). Our results show that BCMS are mainly used to assess the risk of recurrence and to select patients for adjuvant chemotherapy; notably, no consensus has been reached on the lack of utility of BCMS for selecting the type of chemotherapy to administer. Also, there are discrepancies between the recommended and current use of BCMS in clinical practice, with use in certain patient profiles for which there is no supporting evidence. Our study suggests that physician education initiatives are needed to ensure the correct use and interpretation of BCMS to, ultimately, improve management of patients with eBC.
Risk factors for wound healing complications after revascularization for MMD with complete Y-shaped incision
Authors: Wang Chenchao , Li Hongwei , Dong Yang , Wang Hao , Li Dongpeng , Zhao Chengbin , Cao Lei , Sun Kaiwen , Geng Jiefeng , Yang Bo 
Published: February 2023

AbstractMoyamoya disease (MMD) is a chronic occlusive cerebrovascular disease that can be treated with revascularization. Surgery increases the risk of poor wound healing (PWH) due to the impact on the blood supply to the flap. We aimed to analyze risk factors for PWH in MMD with a complete Y-shaped incision. A total of 125 patients with MMD were enrolled in this prospective observational study. The wounds were assessed and measured on the third and seventh days after surgery. The mean age of these patients was 43.3 ± 10.0 years. The ratio of male to female was 1:1.3. 15 (12.0%) patients had incision complications. 5 patients (4.0%) had redness; 2 patients (1.6%) had swelling; 2 patients (1.6%) had fat necrosis; 3 patients (2.4%) had incision infection; and 3 patients (2.4%) had flap necrosis. Student’s t test showed significant differences in BMI (P = 0.040) and fever time (P = 0.050). The standard chi-squared test showed significant differences in incision infection (P = 0.010), suture mode (P = 0.047), and cutting off large branch vessels in the flap (P < 0.001). Multivariate logistic regression analysis suggested that incision infection (P = 0.026, OR 12.958), using a skin stapler (P = 0.030, OR 4.335), cutting off large branch vessels in the flap (P = 0.009, OR 5.227), and BMI (P = 0.027, OR 1.204) were risk factors. The area under the curve for risk factors for PWH on a receiver operating characteristic curve was 0.853. Incision infection, using a skin stapler, higher BMI, and cutting off large branch vessels in the flap are risk factors for PWH.
The clinical characteristics of anemia in native adults living at different altitudes of the Tibetan Plateau
Authors: Fang Jie , Li Ran , Ye Dongdong , Chen Liang , Zhuo Ma Luo Bu , Zhang Yinyin , Zhu Jun , Gao Xiaodong , Xu Pengpeng , Zheng Yu , Li Xiaoyang , You Jianhua , Jiang Chuanhe , Qing Kai , Yue Fei , Li Junmin , Wang Dui Pu Bu , Xue Kai 
Published: February 2023

AbstractTo provide evidence-based medicine references for formulating prevention and control policies in plateau areas, we explore the characteristics of anemia patients in Tibet (the plateau areas of China), especially those located at an altitude above 4500 m. We collected clinical data from 379 Tibetan anemia patients over the age of 18 years. We found those female patients accounted for the majority of Tibetan anemia patients. Almost half of the anemia patients aged from 28 to 47 years. The percentage of severe anemia and extremely severe anemia was 45.4% and 2.4%, respectively. 88.7% of patients are engaged in agriculture and animal husbandry, and 81.5% of patients just graduated from primary school or below. The most common causes of anemia were nutritional anemia, especially iron-deficiency anemia. At high-altitude localities, folic acid-deficiency anemia needs more attention. Overall, this study showed that altitude influences the incidence, severity, and cause of anemia. Peasants and herdsmen, low education levels, young and middle-aged women, and nutrition status should be paid attention to in future anemia control.
Two wild carnivores selectively forage for prey but not amino acids
Authors: Dwyer Georgia K. , Stoffels Rick J. , Silvester Ewen , Rees Gavin N. 
Published: February 2023

AbstractIn nutritional ecology the intake target is the diet that maximises consumer fitness. A key hypothesis of nutritional ecology is that natural selection has acted upon the behavioural and physiological traits of consumers to result in them Selectively Consuming prey to match the Intake Target (SCIT). SCIT has been documented in some herbivores and omnivores, which experience strong heterogeneity in the nutritional quality of available foods. Although carnivores experience a prey community with a much more homogeneous nutrient composition, SCIT by carnivores has nevertheless been deemed highly likely by some researchers. Here we test for SCIT for micronutrients (amino acids) in two freshwater carnivores: the river blackfish and the two-spined blackfish. Although both blackfishes exhibited non-random consumption of prey from the environment, this resulted in non-random consumption of amino acids in only one species, the river blackfish. Non-random consumption of amino acids by river blackfish was not SCIT, but instead an artefact of habitat-specific foraging. We present hypotheses to explain why wild populations of freshwater carnivores may not exhibit SCIT for amino acids. Our work highlights the need for careful, critical tests of the hypotheses and assumptions of nutritional ecology and its application to wild populations.
Rodent activity in municipal waste collection premises in Singapore: an analysis of risk factors using mixed-effects modelling
Authors: Soh Stacy , Chua Chee Heong , Neo Zhi Wei , Kong Marcella , Ong Bee Leng , Aik Joel 
Published: February 2023

AbstractRefuse storage and collection systems are potential sources of food and harbourage areas for rodents which transmit pathogens. We examined the factors associated with rodent activity in public housing municipal waste collection premises in a highly urbanized city-state. We analysed data from April 2019 to March 2020 in mixed-effects logistic regression models to examine the independent factors associated with rodent activity in central refuse chute rooms (CRCs), individual refuse chute (IRC) bin chambers and bin centres. We accounted for within-year patterns, repeated measures and nested effects. We observed a heterogeneous spatial distribution of rodent activity. Rodent droppings were strongly associated with rodent activity in CRCs (aOR: 6.20, 95% CI: 4.20–9.15), bin centres (aOR: 3.61, 95% CI: 1.70–7.64) and IRC bin chambers (aOR: 90.84, 95% CI: 70.13–117.67). Gnaw marks were positively associated with rodent activity in CRCs (aOR: 5.61, 95% CI: 3.55–8.97) and IRC bin chambers (aOR: 2.05, 95% CI: 1.43–2.95), as were rub marks in CRCs (aOR: 5.04, 95% CI: 3.44–7.37) and IRC bin chambers (aOR: 3.07, 95% CI: 1.74–5.42). Each burrow increased the odds of rodent sightings in bin centres (aOR: 1.03, 95% CI: 1.00–1.06). The odds of rodent sightings in an IRC bin chamber increased with every additional bin chute chamber within the same block (aOR: 1.04, 95% CI: 1.01–1.07). We identified several factors that well predicted rodent activity in waste collection premises. Municipal estate managers with limited resources can adopt a risk-based approach in tailoring the focus of their rodent control interventions.