bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of A Frequency-Based Alignment-Free Approach For Phylogeny Reconstruction.
Authors: Hrytsenko Yana , Daniels Noah M. , Schwartz Rachel S. 
Published: February 2022

Abstract
Background: Phylogenies enrich our understanding of how genes, genomes, and species evolve. Traditionally, alignment-based methods are used to construct phylogenies from genetic sequence data; however, this process can be time-consuming when analyzing the large amounts of genomic data available today. Additionally, these analyses face challenges due to differences in genome structure, synteny, and the need to identify similarities in the face of repeated substitutions resulting in loss of phylogenetic information contained in the sequence. Alignment Free (AF) approaches using k-mers (short subsequences) can be an efficient alternative due to their indifference to positional rearrangements in a sequence. However, these approaches may be sensitive to k-mer length and the distance between samples.Results: In this paper, we analyzed the sensitivity of an AF approach based on k-mer frequencies to these challenges using cosine and Euclidean distance metrics for both assembled genomes and unassembled sequencing reads. Quantification of the sensitivity of this AF approach for phylogeny reconstruction to branch length and k-mer length provides a better understanding of the necessary parameter ranges for accurate phylogeny reconstruction. Our results show that a frequency-based AF approach can result in accurate phylogeny reconstruction when using whole genomes, but not stochastically sequenced reads, so long as longer k-mers are used. Conclusions: In this study, we have shown an AF approach for phylogeny reconstruction is robust in analyzing assembled genome data for a range of numbers of substitutions using longer k-mers. Using simulated reads randomly selected from the genome by the Illumina sequencer had a detrimental effect on phylogeny estimation. Additionally, filtering out infrequent k-mers improved the computational efficiency of the method while preserving the accuracy of the results thus suggesting the feasibility of using only a subset of data to improve computational efficiency in cases where large sets of genome-scale data are analyzed.
E-Health and M-Health Interventions to Improve Eating Behaviour of People with a Lower Socioeconomic Position: A Scoping Review of Behaviour Change Techniques
Authors: Ronteltap Amber , Bukman Andrea J. , Nagelhout Gera E. , Hermans Roel C.J. , Hosper Karen , Haveman-Nies Annemien , Lupker Remko , Bolman Catherine A.W. 
Published: February 2022

Abstract
Specific approaches are needed to reach and support people with a lower socioeconomic position (SEP) to achieve healthier eating behaviours. There is a growing body of evidence suggesting that e-health tools exhibit potential to address these needs because of its specific features that enable application of various behaviour change techniques (BCTs). The overall aim of this scoping review is to identify the BCTs that are used in diet-related e-health and m-health interventions targeted at people with a low SEP. The systematic search was performed in 3 databases, using terms related to e/m-health, diet quality and socioeconomic position. A total of 17 full text papers were included. The average number of BCTs per intervention was 6.9 (ranged 3-15). BCTs from the cluster ‘Goals and planning’ were applied most often (25x), followed by the clusters ‘Shaping knowledge’ (18x) and ‘Natural consequences’ (18x). Other frequently applied BCT clusters were ‘Feedback and monitoring’ (15x) and ‘Comparison of behaviour’ (13x). Whereas some BCTs were frequently applied, such as goal setting, others were rarely used, such as social support. Most studies (n=13) observed a positive effect of the intervention on eating behaviour (e.g. having breakfast) in the low SEP group, but this was not clearly associated with the number or type of applied BCTs. In conclusion, more intervention studies focused on people with a low SEP are needed to draw firm conclusions as to which BCTs are effective in improving their diet quality. Also, further research should investigate combinations of BCTs, the intervention design and context, and the use of multicomponent approaches. We encourage intervention developers and researchers to describe interventions more thoroughly, following the systematics of a behaviour change taxonomy, and to select BCTs knowingly.
Time-resolved smoothness of distributed brain activity tracks conscious states and unifies emergent neural phenomena
Authors: Nanda Aditya , Johnson Graham , Mu Yu , Ahrens Misha , Chang Catie , Englot Dario , Breakspear Michael , Rubinov Mikail 
Published: February 2022

Abstract
Much of systems neuroscience posits that emergent neural phenomena underpin important aspects of brain function. Studies in the field variously emphasize the importance of distinct emergent phenomena, including weakly stable dynamics, arrhythmic 1/f activity, long-range temporal correlations, and scale-free avalanche statistics. Few studies, however, have sought to reconcile these often abstract phenomena with interpretable properties of neural activity. Here, we developed a method to efficiently and unbiasedly generate model data constrained by interpretable empirical features in long multiregional neurophysiological recordings. We used this method to ground several major emergent neural phenomena to time-resolved smoothness, the correlation of distributed brain activity between adjacent timepoints. We first found that in electrocorticography recordings, time-resolved smoothness closely tracked transitions between conscious and anesthetized states. We then showed that a minimal model constrained by time-resolved smoothness, variance, and mean, captured dynamical and statistical emergent neural phenomena across modalities and species. Our results thus decouple major emergent neural phenomena from network mechanisms of brain function, and instead couple these phenomena to spatially nonspecific, time-resolved changes of brain activity. These results anchor several theoretical frameworks to a single interpretable property of the neurophysiological signal and, in this way, ultimately help bridge abstract theories of brain function with observed properties of brain activity.
Thermoelectric signature of quantum critical phase
in a doped spin liquid candidate
Authors: Wakamatsu Kodai , Suzuki Yuji , Fujii Takenori , Miyagawa Kazuya , Taniguchi Hiromi , Kanoda Kazushi 
Published: February 2022

Abstract
Quantum spin liquid is a nontrivial magnetic state of longstanding interest, in which spins are strongly correlated and entangled but do not order1, 2; further intriguing is its doped version, which possibly hosts strange metal and unconventional superconductivity3. Promising and currently the only candidate of the doped spin liquid is a triangular-lattice organic conductor, κ-(BEDT-TTF)4Hg2.89Br8, recently found to hold metallicity, spin-liquid-like magnetism and BEC-like superconductivity4-6. The nature of the metallic state with the spin-liquid behaviour is awaiting to be further clarified. Here, we report the thermoelectric signature that mobile holes in the spin liquid background is in a quantum critical state and it pertains to the BEC-like superconductivity. The Seebeck coefficient divided by temperature, S/T, is enhanced on cooling with logarithmic divergence indicative of quantum criticality. Furthermore, the logarithmic enhancement is correlated with the superconducting transition temperature under pressure variation, and the temperature and magnetic field profile of S/T upon the superconducting transition change with pressure in a consistent way with the previously suggested BEC-BCS crossover. The present results reveal that the quantum criticality in a doped spin liquid emerges in a phase, not at a point, and is involved in the unconventional BEC-like nature.
Aptamer Loaded Superparamagnetic Beads For Selective Capturing And Gentle Release of Activated Protein C
Authors: Hamedani Nasim Shahidi , Happich Felix Lucian , Klein Eva-Maria , Rühl Heiko , Mayer Günter , Müller Jens , Pötzsch Bernd 
Published: February 2022

Abstract
Activated protein C (APC) is a serine protease with anticoagulant and cytoprotective activities which make it an attractive target for diagnostic and therapeutic applications. In this work, we present one-step activation of APC from a commercial source of protein C (PC, Ceprotin®) followed by rapid and efficient purification using the APC-specific aptamer HS02-52G loaded on MyOne superparamagnetic beads. Due to the Ca2+-dependent binding of APC to HS02-52G, an efficient capturing of APC was applied in the presence of Ca2+ ions, while a gentle release of captured APC was achieved in the elution buffer containing low EDTA concentration (5 mM). The captured and eluted APC showed more than 95% purity according to an enzyme-linked fluorescent assay (VIDAS® Protein C). The purification yield of 45% was calculated when 4.2 µg APC was used, however this yield reduced to 21% if the starting amount of PC increased to 28.5 µg. Altogether, this method is recommended for rapid and efficient PC activation and APC purification. The purified APC can be used directly for downstream processes where high concentration of pure and active APC is needed.
Intensifying Camel Productivity through Integrated Control of Surra within the Somali ecosystem of the Horn of Africa
Authors: Nuur Abdullahi Sheikh Mohamed , Awale Mousa Mohamed , Hersi Abdullahi A. , Awale Ismail A. , Awale Nashaad Fa. , Ali Yasir Hu. , Ismail Mohamoud Yu. , Chemuliti Judith K. 
Published: February 2022

Abstract
A two phase (10 November to 21 December 2019 dry season, and 6 June to 11 July 2021 rainy season) cross sectional Parasitological, Haematological and Entomological survey was carried out in Somaliland’s Saahil and Togdheer regions. A total of 390 and 395 camels were bled during first and second phase respectively to determine the prevalence of camel trypanosomosis and trap transmitting vectors. Thin and thick smears from Buffy coat and from direct venous blood samples were screened. Out of 390, only 2 camels (0.5%) from Saahil region were positive in first phase while out of 395, 68 camels, 67 Saahil and 1 Togdheer (17.2 %) were positive in second phase. Prevalence of Trypanosoma evansi (T. evansi) infection recorded were (10.6 %), (5.3%) and 1.3% for camels with poor, fair and good body conditions respectively and were statistically significant (P =0.002). No significant prevalence differences between sex and age recorded. Micro-hematocrit method was used to determine packed cell volume (PCV). Animals with (PCV) < 25% were considered anemic and prevalence was negatively correlated to PCV. Biting flies (vectors) were trapped using NZI trap. Traps were set and emptied 48 hours post setting in both regions and phases. Two families of vectors- Tabanidae and Muscidae were identified. The study revealed camel trypanosomosis is enzootic in the region. The disease and its vectors are strongly related to ecology and season.
A multicenter retrospective study of 239 patients aged over 70 years with diffuse large B-cell lymphoma in China
Authors: Yang Chunli , Li Qiaoer , Li Li , Xie Ke , Zhang Yakun , Han Yunwei , Zou Liqun 
Published: February 2022

Abstract
BackgroundDiffuse large B-cell lymphoma (DLBCL) is the most common aggressive lymphoma subtype worldwide and frequently occurs in the elderly population. However, there was a lack of large series of data regarding the clinical profiles of over 70 years in DLBCL patients in China. We aim to summarize this population’s clinical features and survival outcomes in the real world.MethodsThe multicenter retrospective study was conducted in Western China from Jan 2012 to July 2020 to investigate clinical features and survival outcomes of 239 DLBCL patients over 70 years. All patients underwent pre-treatment evaluations, treatment, and follow-up at local hospitals. The primary endpoints of this study were progression-free survival (PFS) rate and overall survival (OS) rate at two years. The second endpoints included median PFS and OS, 5-year PFS and OS rates, and adverse events during treatment.ResultsWith a median follow-up of 50 months (range, 1-102), the 2-year PFS and OS rates were 53.0% (95% CI: 46.5-59.5) and 65.5% (95% CI: 59.4-71.2). The median PFS and OS were 42.1 months and 96.4 months, and the 5-year PFS and OS rates were 44.7% (95% CI: 38.0-51.4) and 56.1% (95% CI: 49.4-62.8). Hematological toxicities were the most common adverse effects in this study, accounting for 90.4%, and leukopenia was the most frequently observed ≥ grade 3 events. Moreover, we observed that no rituximab-containing treatment and chemotherapy cycles < 6 were significantly associated with inferior survival. Furthermore, in the younger than 80 years group, reduced chemotherapy dose was associated with remarked shorter OS; the 2-y OS rate was 74.4% (95% CI: 67.0-81.8) in full dose group in comparison with 67.1% (95% CI: 51.8-82.4) in decreased dose group, p 0.044.ConclusionsOur study indicated that rituximab, enough treatment cycles, full chemotherapy dose should be administered for elderly DLBCL patients under the balance of benefit and risk.
Influence of monocalcium phosphate on the properties of bioactive magnesium phosphate bone cement
Authors: Lv Shaochun , Qu Tianyu , Al-Ward Hisham , Mu Liting , Qiu Hongbin , Zhang Yunlong 
Published: February 2022

Abstract
Background: The bone defects caused by different reasons led to deformity and dysfunction of human body. Considering the need for clinical application, it was essential for bone regeneration to exploit a scaffold with bioactive bone cement. In this paper, we fabricated bioactive magnesium phosphate bone cement (BMPC) at room temperature, then it was set at 37℃ and 100% humidity for 2h. Methods: The process was as follows. MgO was formed by calcining Mg2(OH)2CO3, MgO, KH2PO4 and carboxymethyl chitosan were mixed to form magnesium phosphate bone cement(MPC), then Ca(H2PO4)2 was added to neutralize alkaline product after MPC hydration to fabricate bioactive magnesium phosphate bone cement (BMPC). The influence of doped content of Ca(H2PO4)2 on the properties of bone cement was discussed. Results: The results showed that Ca(H2PO4)2 and carboxymethyl chitosan can adjust the setting time of bone cement within the scope of 8 minute and 25 minute. The compressive strength increased first and then decreased. After 48h without additional pressure, the compressive strength reached the maximum value, so it was about of 38.6 MPa. Ca(H2PO4)2 and carboxymethyl chitosan can play a synergistic role in regulating the BMPC properties. BMPC was degradable in the simulated body fluid (SBF). The results of cytotoxicity experiment and laser confocal microscopy experiment indicated that BMPC fabricated at room temperature had better biocompatibility and degradability, which was more consistent with clinical operation requirement.Conclusions: BMPC can be used as a promising orthopedic material, and it can meet with the needs for repairing bone defects.
A New Method for Axis Adjustment of the Hydro-generator Unit Using Machine Learning
Authors: Cao Jie , Li Yang , Qu Zhaoyang , Dong Yunchang , Liu Yaowei , Zhang Ruxuan 
Published: February 2022

Abstract
The power quality and efficiency of the hydro-power station depend on the stable operation of the hydro-generator unit, which needs to continue to operate and it is prone to axis failure. Therefore, to adopt effective axis adjustment technology to eliminate faults. This paper proposes a new method for axis adjustment of hydro-generator unit based on an improved grey prediction model and swarms intelligence optimization neural network. First of all, it proposes a sequence acceleration translation and mean value transformation method, which is used to pre-process the axis net total swing sequence that exhibits oscillating fluctuations. It uses e1 and e2 factor transformation to establish an improved axis net total swing gray prediction model. Then, the advanced flamingo search algorithm is used to search the maximum value of the sine function of the net total pendulum of the axis, and the axis adjustment orientation is obtained. This method solves the problem that GM(1, 1) can only be predicted by monotone sequence in the past and the problem that the search algorithm is easy to fall into local optimum, effectively improves the calculation efficiency of axis and shorts the search time. Simulation examples show that the proposed method can significantly improve accuracy of axis adjustment. This method greatly improves the efficiency of azimuth search for axis adjustment.
Efficacy and safety of anti-PD-1 monotherapy and combination therapy in Chinese advanced Gastric cancer: a real-world study
Authors: Li Tao , Liu Tingting , Zhao Lei , Liu Lu , Zheng Xuan , Wang Jinliang , Zhang Fan , Hu Yi 
Published: February 2022

Abstract
Purpose: Anti-PD-1 inhibitor, pembrolizumab, has been approved for the treatment of locally advanced or metastatic gastric or gastroesophageal junction cancer (GC/GEJC) patients. Our study aimed to evaluate the efficacy and safety profile of anti-PD-1-based treatment in Chinese advanced or metastatic GC/GEJCs and population with poor clinical conditions in a real-world setting.Methods: A retrospective cohort study was conducted and 54 patients were identified and included in our analysis, including 19 patients treated with anti-PD-1 monotherapy and 35 patients treated with anti-PD-1 combination therapy. Demographic and clinical information were evaluated. Clinical response, survival outcomes and safety profile were measured and analyzed. Results: In overall cohort, median overall survival (OS) was 11.10 months (95%CI, 7.05-15.15) and median progression-free survival (PFS) was 3.93 months (95%CI, 2.47-5.39). 16.7% patients reached clinical response and 72.2% patients got disease control. Prolonged OS and PFS and increased clinical response were observed in combination group compared with monotherapy group, although statistical significance was not reached. In subgroups with live metastases or elevated baseline NLR level, combination therapy outperformed anti-PD-1 alone in survival outcomes. 50% and 16.7% of the overall cohort experienced treatment-related adverse events (TRAEs) of any grade and grade 3-5. Conclusions: Anti-PD-1-based monotherapy and combination therapy showed favorable survival outcomes and manageable safety profile in advanced or metastatic GC/GEJCs. Specific population might benefit from combination therapy. Further study with larger sample size is needed.
Silage of Rehydrated Corn And Sorghum Grain Without And With Amylolytic Enzyme
Authors: Silva Janaina Tayna , De Oliveira Euclides Reuter , Gandra Jefferson Rodrigues , Neves Nathálie Ferreira , Gabriel Andrea Maria de Araújo , Monção Flávio Pinto , Okadad Elaine Sayuri Miyagi , Andrade Wagner da Paz , Fernandes Alexandre Rodrigues Mendes , Peixoto Eduardo Lucas Terra 
Published: February 2022

Abstract
Aimed of this work was to evaluate rehydrated corn and sorghum grains silages, with and without α-AMYLASE, on fermentation profile, nutritional value, digestion and metabolism on diets for sheep. Two experiments were conducted. In the first experiment 28 silos were divided into: 1- RSGS (rehydrated sorghum grain silage); 2- RSGS+A (rehydrated sorghum grain silage + amylase,); 3- RCGS (rehydrated corn grain silage); 4 RCGS+A (rehydrated corn kernel silage + amylase). In experiment II, 12 lambs were distributed in: RSGS; RSGS+A; RCGS; RCGS+A. In experiment I, there was an effect of grain x enzyme interaction for GL MN. The enzyme reduced the NFC content. In experiment II intake of DM kg/day was not affected by the starch content in the diet, with an average of 1.2 kg/day meaning that the type of grain and the enzyme had no influence on the intake of animals. There was an interaction for the intake of starch (kg/day), blood urea and N-NH 3. Lambs fed with RCGS+A had a higher concentration of ruminal ammonia. The use of enzymes improved the fermentation profile of the silages. RSGS can replace RCGS in sheep feed without modifying nutrient intake and digestibility.
Comprehensive Study of Semi-Supervised Learning for DNA Methylation-based Supervised Classification of Central Nervous System Tumors
Authors: Tran Quynh T. , Alom Md Zahangir , Orr Brent A. 
Published: February 2022

Abstract
Background: Optimal treatment for cancer patients relies on accurate pathological diagnosis. The world health organization has defined almost 100 known central nervous system (CNS) tumors, making the histopathological diagnostic process particularly challenging. To help reduce variability, validation costs, and standardize the histopathological diagnostic process, supervised machine learning techniques using epigenetic data have been developed. These methods require large labeled training data sets to obtain clinically acceptable classification accuracy. However, labeling pathology data for machine learning models is time-consuming and resource-intensive, especially for rare tumor types. On the other hand, there is now abundance of unlabeled epigenetic data across multiple databases. To maximize the utility of both labeled and unlabeled data, semi-supervised learning (SSL) approach has been proposed and shown to be effective in genomic field. However, it has not yet been explored with epigenetic data nor demonstrated beneficial to CNS tumor classification.Results: This paper explores the application of semi-supervised machine learning on methylation data to improve accuracy of supervised learning models in classifying CNS tumors. We comprehensively evaluated 11 SSL methods and developed a novel combination approach including a self-training with editing using support vector machine (SETRED-SVM) as the base learner model with an L2-penalized, multinomial logistic regression model to obtain high confidence labels from a small labeled instances. Results across 8 differently trained random forest and neural net models show that SETRED-SVM followed with multinomial logistic regression approach is able to produce high confidence training data set, leading to a statiscally significant increase in prediction accuracy of 82 CNS tumors.Conclusions: The proposed combination of semi-supervised technique and multinomial logistic regression holds the potential to leverage the abundant publically available unlabeled methylation data effectively. Such an approach is highly beneficial in providing additional training examples, especially for scarce tumor types, to boost the prediction accuracy of supervised models.