bluuebunny/crossref_metadata_2025_split huggingface dataset:
RDMA Based Congestion Control Strategy for DML Training Optimization in Data Center Networks
Authors: Wu Jiagui , Qin Yang , Yang Weihong , Li Ruonan 
Published: July 2022

Abstract

Distributed Machine Learning (DML) is one of the important means to accelerate the training of machine learning models. However, the Remote Direct Memory Access (RDMA) technology applied in the data center network cannot well support the communication of DML during parameter synchronization, and there will be relatively large communication overhead. The TMDML (Traffic Management for DML) proposed in this paper records and maintains the state of the data stream by the network nodes, and allocates the bandwidth according to the network state. TMDML achieves higher communication efficiency while reducing the total time to complete DML tasks by alleviating the slow flow lag problem. On this basis, we design TMDML-NIC and TMDML-Switch to meet the deployment requirements of different network equipment. At the same time, we propose the fluid model of TMDML, and the experiments show that the fluid model is in good agreement with the realization method. Through the fluid model, we can not only visually see the changes of important indicators such as flow rate, but also predict these indicators to a certain extent, and can also use it to better optimize the protocol parameters. We conduct simulation experiments on DCQCN and TMDML for different deep learning models and different topologies, respectively. The experimental results show that, compared with DCQCN, TMDML reduces the number of ECNs per switch, which indicates that TMDML can better alleviate the congestion state in the network. The communication overhead caused by parameter synchronization is all reduced in our training tasks. Especially in the Fat-Tree model, there is at least a 32% reduction. This ratio will be higher on more time-consuming models and topologies with more nodes.
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.
Authors: Elofsson Arne , Bryant Patrick , Pozzati Gabriele , Zhu Wensi , Shenoy Aditi , Kundrotas Petras 
Published: July 2022

Abstract
AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. Here we show that one can predict the structure of large complexes starting from predictions of subcomponents. We assemble 91 out of 175 complexes with 10–30 chains from predicted subcomponents using Monte Carlo tree search, with a median TM-score of 0.51. There are 30 highly accurate complexes (TM-score ≥ 0.8, 33% of complete assemblies). We create a scoring function, mpDockQ, that can distinguish if assemblies are complete and predict their accuracy. We find that complexes containing symmetry are accurately assembled, while asymmetrical complexes remain challenging. The method is freely available and accesible as a Colab notebook https://colab.research.google.com/github/patrickbryant1/MoLPC/blob/master/MoLPC.ipynb.
Vapor-phase (p, ρ, T ) Behavior of Difluoromethane (R32)+ Trifluoroiodomethane (R13I1), Pentafluoroethane(R125) + R13I1, and R32 + R125 + R13I1 mixtures: Experimental Measurements Based on the IsochoricMethod and Verification with a Generalized VirialEquation of State
Authors: Akasaka Ryo , Kayukawa Yohei , Higashi Yukihiro 
Published: July 2022

Abstract
Mixing R13I1 with flammable or weakly-flammable refrigerants is an approach to reduce both their flammability and global warming potential(GWP); however, thermodynamic property data of mixtures containing R13I1are currently scarce. In this work, experimental measurements were performed for the (p, ρ, T) behavior in the vapor phase of R32 + R13I1, R125 + R13I1,and R32 + R125 + R13I1 mixtures. The measurements were made at temperatures from 300 K to 400 K and pressures up to 6.3 MPa, and 44 data points were obtained for the R32 + R13I1 mixture and 25 data points for theR125 + R13I1 mixture. For the ternary mixture, 25 data points were obtained at the composition of R466A (R32:R125:R13I1 = 49:11.5:39.5 mass%). The validity of the experimental data was verified by comparing to the virial equation of state generalized for nonpolar or weakly polar fluids based on the corresponding states principle. The comparison showed that deviations between the experimental and calculated pressures are generally minor and less scattered; this suggests that the (p, ρ, T) data obtained in this work are reasonable in terms of the law of corresponding states.
Predicting the Need for Intubation Within 3 Hours in the Neonatal Intensive Care Unit Using a Multimodal Deep Neural Network
Authors: Im Jueng-Eun , Park Seung , Kim Yoo-Jin , Yoon Shin Ae , Lee Ji Hyuk 
Published: July 2022

Abstract
Respiratory distress is a common chief complaint in neonates admitted to the neonatal intensive care unit. Despite the increasing use of non-invasive ventilation in neonates with respiratory difficulty, some of them require advanced airway support. Delayed intubation is associated with increased morbidity, particularly in urgent unplanned cases. Early and accurate prediction of the need for intubation may provide more time for preparation and increase safety margins by avoiding the late intubation at high-risk infants. This study aimed to predict the need for intubation within 3 hours in neonates initially managed with non-invasive ventilation for respiratory distress during the first 48 hours of life using a multimodal deep neural network. We developed a multimodal deep neural network model to simultaneously analyze 4 time series data collected at 1-hour intervals and 19 variables including demographic data, physiological parameters, and laboratory values. Evaluating the dataset of 128 neonates with respiratory distress who underwent non-invasive ventilation, our model achieved an area under the curve of 0.917, sensitivity of 85.2%, and specificity of 89.2%. These findings demonstrated that the multimodal model successfully predicted the need for intubation within 3 hours.
Impact of age on the prognosis and decision-making of adjuvant treatment for resectable rectal cancer- a population based analysis
Authors: Wang Lei , Lai Cheng , Zhong Xiaohong , Shao Lingdong , Wu Junxin 
Published: July 2022

Abstract
Background
Different age groups exhibit disparate patterns of epidemiology, clinicopathology, treatment response, and prognosis in relation to rectal cancer (RC), but little is known about the interactions between age and adjuvant treatment (AT) for resectable RC.
Methods
The Surveillance, Epidemiology, and End Results database (SEER) was used to identify patients who had received surgery but not neoadjuvant treatment for rectal adenocarcinoma between 2010 and 2015. Restricted cubic spline (RCS) was used to identify the optimal cut-off value of age for overall survival (OS) and cancer-specific survival (CSS), and then further analysis was performed using Kaplan-Meier (KM) curves and propensity score matching (PSM) stratified by different age groups, pathological stage (pT1 − 2N0, pT3 − 4N0, pT1 − 4N+), and AT modalities including chemotherapy (CT), radiotherapy (RT), and CT + RT.
Results
7951 patients were eligible for this study, and age was found to be an independent risk factor of OS and CSS after adjusted other risk factors (all P < 0.001). 50 years old was identified as the optimal cut-off value for OS and CSS using RCS, and patients aged < 50 years old (early-onset rectal cancer, EORC) have a significantly better prognosis than those aged ≥ 50 years old (late-onset rectal cancer, LORC) before and after PSM (both P < 0.001). Among the EORC patients, only subgroup of pT1 − 4N + was found to be benefited from AT before and after PSM (both P < 0.05), and further analysis showed that this population was only benefited from adjuvant CT in terms of OS (P < 0.05). Among LORC patients, subgroups of pT3 − 4N0 and pT1 − 4N + were both found to be benefited from AT (both P < 0.001). Further analysis showed that adjuvant CT and CT + RT could both significantly improve the OS of these two subgroups (all P < 0.05), but adjuvant RT alone was only found to benefit those staged at pT1 − 4N+ (P < 0.05).
Conclusions
The optimal age threshold for RC patients undergoing direct surgery was 50 years old. Patients with EORC staging at pT1-4N + should receive adjuvant CT + RT. Patients with LORC staging at pT3-4N0 and pT1-4N + should receive adjuvant CT + RT or CT. In addition, adjuvant RT alone could also be an option for selected LORC patients. However, this conclusion deserves further validation by prospective cohorts.
A pilot surveillance report of SARS-CoV-2 rapid antigen test results among volunteers in Germany, 1st week of July 2022
Authors: Stemler Jannik , Salmanton-García Jon , Weise Ben , Többen Christina , Joisten Carolin , Fleig Julian , Cornely Oliver 
Published: July 2022

Abstract
PurposeWe hypothesized that reported SARS-CoV-2 infection numbers are underestimated due to high dark figures as only results from polymerase chain reaction (PCR) tests are incorporated in governmental statistics and testing capacities were further restricted as of July, 2022MethodsA point prevalence investigation was piloted by rapid antigen testing (RAT) among participants of the VACCELERATE volunteer registry. 2400 volunteers were contacted, of which 500 received a RAT including instructions for self-testing in the first week of July, 2022. Results were self-reported via e-mail.Results419 valid RAT results were collected until July 7th, 2022. Between July-1 and July-7, 2022, 7/419 (1.67%) tests were positive. Compared to reports of the German Federal Government, our results suggest a 2.39-fold higher prevalence. Three out of seven positive individuals did not have a PCR test and are therefore likely not to be displayed in governmental statistics.ConclusionOur findings imply that the actual prevalence of SARS-CoV-2 may be higher than detected by current surveillance systems, so that current pandemic surveillance and testing strategies need to be adapted.
Soil Erosion Risk Assessment using Geospatial Techniques
Authors: Ahad Ummar , Ali Umair , Ali Syed Ahmad 
Published: July 2022

Abstract
The present study emphasized the application of geospatial techniques in measurement of drainage and morphometric parameters. Dudhganga-Shaliganga catchment with 7 sub-basins (coded as DS1-DS7) was analyzed to assess the soil erosion risk using detailed measurement of drainage and morphometric parameters using geospatial techniques. Linear, shape and relief parameters were assessed for every sub-basin and accordingly ranks were assigned on the basis of interrelationship with soil erodibility. The stream order up to 6 has been analyzed with drainage density of 1.881 with sub-parallel drainage pattern. As for as the area of interest is concerned, drainage network is controlled by lithological and geomorphic conditions with effect of subsurface structures dominant in SW sub-basins. The sub-basins were divided into high, medium and low category in terms of priority for soil Management and conservation. Ranking reveals that DS1, DS2 and DS6 come under very high soil erosion susceptibility. Existence of these sub-basins towards Pir-Panjal side having high altitudinal, high slope and deep valley topography enhance soil erosion risk supported by deforestation, unmannered cultivation on hill slopes and changing face of landscape by human activities. Besides, the sub-basins showing higher erosion rick have higher concentration of lineaments which acts as weak planes and allows easy water flow and increases chances of landslides by lubrication. Consecutively, soil erosion during heavy rain fall also gives birth to siltation problems in the plainer low lying areas as said above, which is a very serious problem to eradicate. Thus, morphotectonic and morphometric analysis applied has given an importance inferences related to soil erosion risk assessment in the area.
Long-term treatment outcomes of pediatric low-grade gliomas treated at a university-based hospital
Authors: Jujui-eam Apisak , Sirachainan Nongnuch , Hongeng Suradej , Hansasuta Ake , Boongird Attaporn , Tritanon Oranan , Dhanachai Mantana , Swangsilpa Thiti , Ruangkanchanasetr Rawee , Worawongsakul Rasin , Puataweepong Putipun 
Published: July 2022

Abstract
Purpose
A multimodality approach is generally considered for pediatric low-grade gliomas (LGG); however, the optimal management remains uncertain. The objective of the study was to evaluate treatment outcomes of pediatric LGG, focusing on long-term survival and factors related to outcomes.
Methods
A retrospective review of 77 pediatric LGG cases treated at Ramathibodi Hospital, Thailand between 2000 and 2018 was performed. The inclusion criteria were all pediatric LGG cases aged ≤ 15 years. Diffuse intrinsic pontine gliomas and spinal cord tumors were excluded.
Results
The median follow-up time was 8.2 years (range, 0.6–19.7). The median age at diagnosis was 6.2 years (interquartile range, 3.6–11.4). Treatments included surgery (71%), chemotherapy (40%), and radiation therapy (14%). The 10-year overall survival (OS) and 10-year progression-free survival were 94% and 59%, respectively, for the entire cohort. The 10-year OS was 100% in three subgroups of patients: pilocytic subtype, WHO grade 1 tumors, and receipt of gross total resection. After multivariable analysis, older age and no surgery had a significant negative impact on OS.
Conclusions
Excellent outcomes can be achieved in pediatric LGG patients using a multidisciplinary approach. Gross total resection is the standard primary treatment. Chemotherapy is the alternative standard treatment in incomplete resection cases, unresectable patients, or patients with progressive disease. Radiation therapy should be reserved as a salvage treatment option because of late complications that usually affect patients’ quality of life.
Paracoccus marinaquae sp. nov., isolated from coastal water of the Yellow Sea
Authors: Xue Hua-Peng , Fu Zi-Yue , He Wei , Wang Lei , Li Wen-Jun , Zhang Ai Hua , Huang Jian-Ke , Zhang Dao-Feng , Zhao Zhe 
Published: July 2022

Abstract
A Gram-stain-negative, non-motile and coccoid bacterial strain, designated XHP0099T, was isolated from coastal water of the Yellow Sea, China. Growth occurred at 20–37°C (optimum, 28°C), pH 5.0–9.0 (optimum, pH 7.0–8.0), and with 0–7.0% NaCl (optimum, 2.0–3.0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XHP0099T was related to members of the genus Paracoccus and shared highest sequence similarity with P. siganidrum M26T (98.2%), followed by P. alkanivorans 4-2T (97.6%) and P. alkenifer DSM 11593T (97.4%). The major cellular fatty acids (＞10%) were summed feature 8 (C18:1 ω7c/C18:1 ω6c), and C18:0. The major isoprenoid quinone was Q-10 and the polar lipids contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), aminolipid (AL) and unidentified polar lipid (L). The average nucleotide identity values between strain XHP0099T and P. siganidrum M26T, P. alkanivorans 4-2T, P. alkenifer DSM 11593T and P. saliphilus DSM 18447T were 81.41%, 80.13%, 75.77% and 78.27%, respectively. The digital DNA–DNA hybridization values between strain XHP0099T with P. siganidrum M26T, P. alkanivorans 4-2T, P. alkenifer DSM 11593T and P. saliphilus DSM 18447T were 24.10%, 23.00%, 20.80 % and 21.20%, respectively. The G+C content of the genomic DNA of strain XHP0099T was 66.0%. Based on the phenotypic, phylogenetic, biochemical and chemotaxonomic analysis, strain XHP0099T represents a novel species of the genus Paracoccus, for which the name Paracoccus marinaquae sp. nov. is proposed. The type strain is XHP0099T (=JCM 34661T=GDMCC 1.2414T=MCCC 1K05846T).
On the traces of lost identities: chronological, anthropological and taphonomic analyses of the Late Neolithic/Early Eneolithic fragmented and commingled human remains from the Farneto rock shelter (Bologna, Northern Italy)
Authors: Nicolosi Teresa , Mariotti Valentina , Talamo Sahra , Miari Monica , Minarini Laura , Nenzioni Gabriele , Lenzi Fiamma , Pietrobelli Annalisa , Sorrentino Rita , Benazzi Stefano , Belcastro Maria Giovanna 
Published: July 2022

Abstract
The present study examines the prehistoric human skeletal remains retrieved starting from the 20s of the XX century in the deposit of the Farneto rock shelter, situated in the area of the ‘Parco dei Gessi Bolognesi e Calanchi dell’Abbadessa’ (San Lazzaro di Savena, Bologna, Northern Italy). An exact dating and a reliable interpretation of the assemblage had not been reached so far because of the lack of contextual data useful for dating purposes, the inaccurate recovery procedures of the remains, as well as their state of preservation. In fact, the skeletal remains from the Farneto rock shelter are highly fragmented and commingled, whereas reliable information about their original position and their recovery procedures are not available. Despite these difficulties, radiocarbon analyses allowed to clarify the precise dating of the remains, which date back to a final phase of the Neolithic and an early phase of the Eneolithic period in Northern Italy, testifying an early use of natural cavities for funerary purposes in the area. Moreover, the anthropological and taphonomic study of the skeletal remains shed light on the biological profile of the individuals and on some events that occurred after their death. In particular, the analysis of peri mortem lesions highlighted the existence of intentional interventions related to corpse treatment, referable to dismembering/disarticulation and scarnification, i.e., cleaning of bones from soft tissues. Finally, the comparison with other Neo/Eneolithic funerary contexts in Central and Northern Italy enabled a better understanding of these complex ritual practices.
Association between the number of remaining teeth and need for long-term care or support needs among generally healthy older adults in Japan
Authors: Kakei Yasumasa , Kagimura Tatsuo , Yamamoto Yasuji , Osaki Tohmi , Kajita Hiroyuki , Kojima Shinsuke , Kowa Hisatomo , Kawabata Miyuki , Hasegawa Takumi , Akashi Masaya , Nagai Yoji 
Published: July 2022

Abstract
Objectives: Japan has the largest super-aged population worldwide. As long-term care and support for community-dwelling older adults have considerable healthcare and socioeconomic implications, population-based projects are exploring strategies for prevention and early detection of physical and cognitive decline. The Frail Kenshin health checkup program of Kobe city includes citizens aged 64 or 65 years. Materials and methods: Overall, 1508 subjects of the program between August 2017 and March 2018 were included. Frail Kenshin data were analyzed to examine associations between the number of remaining teeth with Cognitive Functional Instrument Self and European Quality of Life Five Dimension questionnaire scores, and near future long-term care need certification. The number of teeth was identified from the Frail Check data; mastication scores and number of chewable foods were also assessed.Results: Reduced numbers of remaining teeth were significantly associated with various measures of general frailty, including motor function, oral function, prevention of seclusion, memory, mental health, mastication scores, total number of chewable foods, and body mass index (p<0.001, all). They were also associated with decreased calf and standing up test scores, worsening in European Quality of Life Five Dimension visual analogue scale scores, degree of mobility, and regular activities (p<0.001, all). Decreased numbers of remaining teeth were associated with increased frequency of long-term care or support need certification (p<0.001). Conclusion: Loss of teeth appears to be associated with long-term care or support needs among community-dwelling older individuals. Clinical relevance: Community-dwelling older adults with loss of teeth require careful monitoring for long-term care needs.
Clinical feature analysis of pneumonia caused by Tropheryma Whipplei
Authors: Lin Jiaping , Ou Yang , Yu Xiaoling , Lai Yanjin , Lai Guoxiang , Chen Lihong , Wang Bin , Shi Yixian , Lin Xiuhua 
Published: July 2022

Abstract
Background: Whipple's Disease (WD) is a rare infection caused by Tropheryma whipplei (TW), which affects multiple organs. When the infection invades the respiratory system, severe respiratory failure can be induced. However, due to extremely low prevalence and insufficient awareness, the disease is easily ignored by practitioners. Recently, we found a case of severe pneumonia with TW infection with respiratory failure induced. We combined published cases to perform a retrospective analysis of the clinical features of pneumonia caused by TW, intending to provide a reference for the treatment of WD.Methods: 11 cases of pulmonary TW infection were retrieved from the literature (1992-2022). Together with the single case identified in our hospital, 12 cases were retrospectively analyzed for risk factors, clinical manifestations, diagnosis and treatment, and outcomes.Results: Pulmonary TW infection was more prevalent in middle-aged men without underlying diseases (9/12, 75%). It usually manifested as respiratory symptoms such as cough (6/12, 50%), dyspnoea (7/12, 58.33%), and chest pain (2/12, 16.67%), which can be accompanied by or only manifested as digestive system symptoms, joint pain, fever, and other extrapulmonary symptoms. Pulmonary imaging findings were nonspecific, presenting various alterations, including multiple ground-glass opacities, consolidations, nodules, cavities in both lungs, as well as pleural effusion, interstitial pneumonia, and acute fibrinous and organizing pneumonia. Based on traditional clinical experience, Pulmonary TW infection can be treated by standardized anti-infective therapies.Conclusions: The clinical manifestations and pulmonary imaging findings of Pulmonary TW infection were diverse and non-specific. Hence, it can be easily missed or misdiagnosed. Significant efficacy can be achieved with prompt diagnosis and effective medication, thus more attention should be paid to this disease. To our knowledge, this is the first retrospective study concerning the clinical features of Pulmonary TW infection to date. Nevertheless, the number of cases presented here was small, which requires the supplementation of more clinical data in the future.