bluuebunny/crossref_metadata_2025_split huggingface dataset:
L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force
Authors: Hwang Sung-Yeon , Jung Hyunchul , Mun Seyoung , Lee Sungwon , Park Kiwon , Baek S. Chan , Moon Hyungseok C. , Kim Hyewon , Kim Baekgyu , Choi Yongkuk , Go Young-Hyun , Tang Wanxiangfu , Choi Jongsu , Choi Jung Kyoon , Cha Hyuk-Jin , Park Hye Yoon , Liang Ping , Kim V. Narry , Han Kyudong , Ahn Kwangseog 
Published: February 2021

AbstractL1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of L1, which exploits RNA m6A modification. We discover that m6A ‘writer’ METTL3 facilitates L1 retrotransposition, whereas m6A ‘eraser’ ALKBH5 suppresses it. The essential m6A cluster that is located on L1 5′ UTR serves as a docking site for eukaryotic initiation factor 3 (eIF3), enhances translational efficiency and promotes the formation of L1 ribonucleoprotein. Furthermore, through the comparative analysis of human- and primate-specific L1 lineages, we find that the most functional m6A motif-containing L1s have been positively selected and became a distinctive feature of evolutionarily young L1s. Thus, our findings demonstrate that L1 retrotransposons hijack the RNA m6A modification system for their successful replication.
Transcriptome and translatome of CO2 fixing acetogens under heterotrophic and autotrophic conditions
Authors: Song Yoseb , Bae Jiyun , Shin Jongoh , Jin Sangrak , Lee Jung-Kul , Kim Sun Chang , Cho Suhyung , Cho Byung-Kwan 
Published: February 2021

AbstractAcetogens are anaerobic bacteria that utilise gaseous feedstocks such as carbon monoxide (CO) and carbon dioxide (CO2) to synthesise biomass and various metabolites via the energetically efficient Wood-Ljungdahl pathway. Because of this pathway, acetogens have been considered as a novel platform to produce biochemicals from gaseous feedstocks, potentially replacing the conventional thermochemical processes. Despite their advantages, a lack of systematic understanding of the transcriptional and translational regulation in acetogens during autotrophic growth limits the rational strain design to produce the desired products. To overcome this problem, we presented RNA sequencing and ribosome profiling data of four acetogens cultivated under heterotrophic and autotrophic conditions, providing data on genome-scale transcriptional and translational responses of acetogens during CO2 fixation. These data facilitate the discovery of regulatory elements embedded in their genomes, which could be utilised to engineer strains to achieve better growth and productivity. We anticipate that these data will expand our understanding of the processes of CO2 fixation and will help in the designing of strains for the desired biochemical production.
Effects of Al substitution by Si in Ti3AlC2 nanolaminate
Authors: Hadi M. A. , Roknuzzaman Md , Nasir M. T. , Monira U. , Naqib S. H. , Chroneos A. , Islam A. K. M. A. , Alarco Jose A. , Ostrikov Kostya 
Published: February 2021

AbstractRecently, a series of high-purity Ti3(Al1−xSix)C2 solid solutions with new compositions (x = 0.0, 0.2, 0.4, 0.6, 0.8 and 1.0) have been reported with interesting mechanical properties. Here, we have employed density functional theory for Ti3(Al1−xSix)C2 solid solutions to calculate a wider range of physical properties including structural, electronic, mechanical, thermal and optical. With the increase of x, a decrease of cell parameters is observed. All elastic constants and moduli increase with x. The Fermi level gradually increases, moving towards and past the upper bound of the pseudogap, when the value of x goes from zero to unity, indicating that the structural stability reduces gradually when the amount of Si increases within the Ti3(Al1−xSix)C2 system. In view of Cauchy pressure, Pugh’s ratio and Poisson’s ratio all compositions of Ti3(Al1−xSix)C2 are brittle in nature. Comparatively, low Debye temperature, lattice thermal conductivity and minimum thermal conductivity of Ti3AlC2 favor it to be a thermal barrier coating material. High melting temperatures implies that the solid solutions Ti3(Al1−xSix)C2 may have potential applications in harsh environments. In the visible region (1.8–3.1 eV), the minimum reflectivity of all compositions for both polarizations is above 45%, which makes them potential coating materials for solar heating reduction.
Contribution of green organs to grain weight in dryland wheat from the 1940s to the 2010s in Shaanxi Province, China
Authors: Sun Yingying , Zhang Suiqi , Yan Jiakun 
Published: February 2021

AbstractEight dryland winter wheat cultivars (Triticum aestivum L.), which were widely cultivated from the 1940s to the 2010s in Shaanxi Province, China, were selected and grown in plots, and two water treatments (irrigation and drought) were used to identify the contribution of ears, leaves and stems to grain weight and grain number associated with cultivar replacement. The plant height and stem dry weight of the dryland wheat decreased significantly during the cultivar replacement process, but there was a remarkable increase in the dry matter translocation of stems under irrigation. Shaded-ear and defoliation treatment could decrease the grain number and grain weight, and the grain weight was more influenced. Both the leaf and ear are important photosynthetic sources for dryland wheat, and the contribution of ear assimilates showed a significant increase over time; however, the contribution of leaf assimilates showed a negative correlation with cultivation over time. The accumulation of stem assimilates and ear photosynthesis both increased the grain weight potential. In the future breeding process, cultivars with more assimilates stored in the stem and greater assimilative capacity of ears, especially a greater contribution of ear assimilates, are expected to increase the grain yield.
Using blood data for the differential diagnosis and prognosis of motor neuron diseases: a new dataset for machine learning applications
Authors: Greco Alberto , Chiesa Maria Rosa , Da Prato Ilaria , Romanelli Anna Maria , Dolciotti Cristina , Cavallini Gabriella , Masciandaro Silvia Maria , Scilingo Enzo Pasquale , Del Carratore Renata , Bongioanni Paolo 
Published: February 2021

AbstractEarly differential diagnosis of several motor neuron diseases (MNDs) is extremely challenging due to the high number of overlapped symptoms. The routine clinical practice is based on clinical history and examination, usually accompanied by electrophysiological tests. However, although previous studies have demonstrated the involvement of altered metabolic pathways, biomarker-based monitoring tools are still far from being applied. In this study, we aim at characterizing and discriminating patients with involvement of both upper and lower motor neurons (i.e., amyotrophic lateral sclerosis (ALS) patients) from those with selective involvement of the lower motor neuron (LMND), by using blood data exclusively. To this end, in the last ten years, we built a database including 692 blood data and related clinical observations from 55 ALS and LMND patients. Each blood sample was described by 108 analytes. Starting from this outstanding number of features, we performed a characterization of the two groups of patients through statistical and classification analyses of blood data. Specifically, we implemented a support vector machine with recursive feature elimination (SVM-RFE) to automatically diagnose each patient into the ALS or LMND groups and to recognize whether they had a fast or slow disease progression. The classification strategy through the RFE algorithm also allowed us to reveal the most informative subset of blood analytes including novel potential biomarkers of MNDs. Our results show that we successfully devised subject-independent classifiers for the differential diagnosis and prognosis of ALS and LMND with remarkable average accuracy (up to 94%), using blood data exclusively.
Forecasting standardized precipitation index using data intelligence models: regional investigation of Bangladesh
Authors: Yaseen Zaher Mundher , Ali Mumtaz , Sharafati Ahmad , Al-Ansari Nadhir , Shahid Shamsuddin 
Published: February 2021

AbstractA noticeable increase in drought frequency and severity has been observed across the globe due to climate change, which attracted scientists in development of drought prediction models for mitigation of impacts. Droughts are usually monitored using drought indices (DIs), most of which are probabilistic and therefore, highly stochastic and non-linear. The current research investigated the capability of different versions of relatively well-explored machine learning (ML) models including random forest (RF), minimum probability machine regression (MPMR), M5 Tree (M5tree), extreme learning machine (ELM) and online sequential-ELM (OSELM) in predicting the most widely used DI known as standardized precipitation index (SPI) at multiple month horizons (i.e., 1, 3, 6 and 12). Models were developed using monthly rainfall data for the period of 1949–2013 at four meteorological stations namely, Barisal, Bogra, Faridpur and Mymensingh, each representing a geographical region of Bangladesh which frequently experiences droughts. The model inputs were decided based on correlation statistics and the prediction capability was evaluated using several statistical metrics including mean square error (MSE), root mean square error (RMSE), mean absolute error (MAE), correlation coefficient (R), Willmott’s Index of agreement (WI), Nash Sutcliffe efficiency (NSE), and Legates and McCabe Index (LM). The results revealed that the proposed models are reliable and robust in predicting droughts in the region. Comparison of the models revealed ELM as the best model in forecasting droughts with minimal RMSE in the range of 0.07–0.85, 0.08–0.76, 0.062–0.80 and 0.042–0.605 for Barisal, Bogra, Faridpur and Mymensingh, respectively for all the SPI scales except one-month SPI for which the RF showed the best performance with minimal RMSE of 0.57, 0.45, 0.59 and 0.42, respectively.
Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation
Authors: Rana Priyanka , Sowmya Arcot , Meijering Erik , Song Yang 
Published: February 2021

AbstractClassification and characterisation of cellular morphological states are vital for understanding cell differentiation, development, proliferation and diverse pathological conditions. As the onset of morphological changes transpires following genetic alterations in the chromatin configuration inside the nucleus, the nuclear texture as one of the low-level properties if detected and quantified accurately has the potential to provide insights on nuclear organisation and enable early diagnosis and prognosis. This study presents a three dimensional (3D) nuclear texture description method for cell nucleus classification and variation measurement in chromatin patterns on the transition to another phenotypic state. The proposed approach includes third plane information using hyperplanes into the design of the Sorted Random Projections (SRP) texture feature and is evaluated on publicly available 3D image datasets of human fibroblast and human prostate cancer cell lines obtained from the Statistics Online Computational Resource. Results show that 3D SRP and 3D Local Binary Pattern provide better classification results than other feature descriptors. In addition, the proposed metrics based on 3D SRP validate the change in intensity and aggregation of heterochromatin on transition to another state and characterise the intermediate and ultimate phenotypic states.
Persistent hepatocyte apoptosis promotes tumorigenesis from diethylnitrosamine-transformed hepatocytes through increased oxidative stress, independent of compensatory liver regeneration
Authors: Nozaki Yasutoshi , Hikita Hayato , Tanaka Satoshi , Fukumoto Kenji , Urabe Makiko , Sato Katsuhiko , Myojin Yuta , Doi Akira , Murai Kazuhiro , Sakane Sadatsugu , Saito Yoshinobu , Kodama Takahiro , Sakamori Ryotaro , Tatsumi Tomohide , Takehara Tetsuo 
Published: February 2021

AbstractHepatocellular carcinoma highly occurs in chronic hepatitis livers, where hepatocyte apoptosis is frequently detected. Apoptosis is a mechanism that eliminates mutated cells. Hepatocyte apoptosis induces compensatory liver regeneration, which is believed to contribute to tumor formation. Hepatocyte-specific Mcl-1 knockout mice (Mcl-1Δhep mice) developed persistent hepatocyte apoptosis and compensatory liver regeneration with increased oxidative stress in adulthood but had not yet developed hepatocyte apoptosis at the age of 2 weeks. When diethylnitrosamine (DEN) was administered to 2-week-old Mcl-1Δhep mice, multiple liver tumors were formed at 4 months, while wild-type mice did not develop any tumors. These tumors contained the B-Raf V637E mutation, indicating that DEN-initiated tumorigenesis was promoted by persistent hepatocyte apoptosis. When N-acetyl-L-cysteine was given from 6 weeks of age, DEN-administered Mcl-1Δhep mice had reduced oxidative stress and suppressed tumorigenesis in the liver but showed no changes in hepatocyte apoptosis or proliferation. In conclusion, enhanced tumor formation from DEN-transformed hepatocytes by persistent hepatocyte apoptosis is mediated by increased oxidative stress, independent of compensatory liver regeneration. For patients with livers harboring transformed cells, the control of oxidative stress may suppress hepatocarcinogenesis based on chronic liver injury.
Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1
Authors: Liu Yi , Ma Jichun , DesJarlais Renee L. , Hagan Rebecca , Rech Jason , Lin David , Liu Changlu , Miller Robyn , Schoellerman Jeffrey , Luo Jinquan , Letavic Michael , Grasberger Bruce , Maher Michael 
Published: February 2021

AbstractAcid-sensing ion channels (ASICs) are proton-gated cation channels critical for neuronal functions. Studies of ASIC1, a major ASIC isoform and proton sensor, have identified acidic pocket, an extracellular region enriched in acidic residues, as a key participant in channel gating. While binding to this region by the venom peptide psalmotoxin modulates channel gating, molecular and structural mechanisms of ASIC gating modulation by small molecules are poorly understood. Here, combining functional, crystallographic, computational and mutational approaches, we show that two structurally distinct small molecules potently and allosterically inhibit channel activation and desensitization by binding at the acidic pocket and stabilizing the closed state of rat/chicken ASIC1. Our work identifies a previously unidentified binding site, elucidates a molecular mechanism of small molecule modulation of ASIC gating, and demonstrates directly the structural basis of such modulation, providing mechanistic and structural insight into ASIC gating, modulation and therapeutic targeting.
Confidence and Training of Speech-Language Pathologists in Cognitive-Communication Disorders: Time to Rethink Graduate Education Models?
Authors: Morrow Emily L. , Turkstra Lyn S. , Duff Melissa C. 
Published: February 2021

Purpose
The purpose of this article is to highlight the need for increased focus on cognitive communication in North American speech-language pathology graduate education models.

Method
We describe key findings from a recent survey of acute care speech-language pathologists (SLPs) in the United States and expand upon the ensuing discussion at the 2020 International Cognitive-Communication Disorders Conference to consider some of the specific challenges of training for cognitive communication and make suggestions for rethinking how to prepare future clinicians to manage cognitive-communication disorders.

Results
Results from the survey of acute care SLPs indicated inconsistent confidence and training in managing cognitive-communication disorders. We discuss the pros and cons of several avenues for improving the consistency of cognitive-communication training, including a standalone cognitive-communication course, integrating cognitive communication in all courses across the speech-language pathology undergraduate and graduate curriculum, and using problem-based learning frameworks to better prepare students as independent thinkers in the area of cognitive communication and beyond.

Conclusions
Cognitive-communication disorders cut across clinical diagnoses and settings and are one of the largest and fastest growing parts of the SLP's scope of practice. Yet, surveys, including the one discussed here, have repeatedly indicated that SLPs do not feel prepared or confident to work with individuals with cognitive-communication disorders. We propose several avenues for increasing educational emphasis on cognitive communication. We hope these ideas will generate discussion and guide decision making to empower SLPs to think critically and step confidently into their roles as leaders in managing the heterogeneous and ever-growing populations of individuals with cognitive-communication disorders.
Heterogeneity Is a Hallmark of Traumatic Brain Injury, Not a Limitation: A New Perspective on Study Design in Rehabilitation Research
Authors: Covington Natalie V. , Duff Melissa C. 
Published: February 2021

Purpose
In both basic science and intervention research in traumatic brain injury (TBI), heterogeneity in the patient population is frequently cited as a limitation and is often interpreted as a factor reducing certainty in the generalizability of research findings and as a source of conflicting findings across studies. Historically, much of TBI research in rehabilitation and cognition has relied upon case–control studies, with small to modest sample sizes. In this context, heterogeneity is indeed a significant limitation. Here, however, we argue that heterogeneity in patient profiles is a hallmark characteristic of TBI and therefore cannot be avoided or ignored. We argue that this inherent heterogeneity must be acknowledged and accounted for prior to study design. Fortunately, advances in statistical methods and computing power allow researchers to leverage heterogeneity, rather than be constrained by it.

Method
In this article, we review sources of heterogeneity that contribute to challenges in TBI research, highlight methodological advances in statistical analysis and in other fields with high degrees of heterogeneity (e.g., psychiatry) that may be fruitfully applied to decomposing heterogeneity in TBI, and offer an example from our research group incorporating this approach.

Conclusion
Only by adopting new methodological approaches can we advance the science of rehabilitation following TBI in ways that will impact clinical practice and inform decision making, allowing us to understand and respond to the range of individual differences that are a hallmark in this population.
The Combined Burden of Hearing Loss and Cognitive Impairment in a Group Care Setting for Older Adults
Authors: Mamo Sara K. , Wheeler Kara A. 
Published: February 2021

Purpose
The purpose of the current study is to better characterize the medical and social health characteristics of older adults in a long-term group care setting and consider the impact of the dual burden of hearing loss and cognitive impairment.

Method

This descriptive analysis of a convenience sample of 160 adults (
M
age
= 74 years, age range: 59.8–99.7) participating in Program for All-inclusive Care for the Elderly programs in Massachusetts and Rhode Island included data from hearing testing, questionnaires, and medical chart review. Using descriptive statistics, groups are compared across a range of demographic and health variables on the categorical bases of hearing loss and cognitive status.

Results
Results suggest that hearing loss and cognitive impairment are highly prevalent among this sample of older adults. Forty-three percent of this sample has at least a mild hearing loss in the better hearing ear in addition to cognitive impairment. Descriptive analyses across demographic and health variables suggest there are few differences between those with and without cognitive impairment when compared within degree of hearing loss categories in this convenience sample. Across all participants, there was a high prevalence of other chronic conditions, most notably diabetes (59%), hypertension (90%), cardiovascular disease (80%), and depression (67%).

Conclusions
In this sample, there were not significant differences on demographic and health variables between the cognitive impairment groups when considered within their degree of hearing loss; however, the prevalence of the dual burden of hearing loss and cognitive impairment in this sample is high. Clinicians serving older adults, especially those accessing group care services, should be cognizant of the high burden of multiple chronic conditions and plan care that can be integrated into a comprehensive approach.
Numerical Simulation for Time Dependent Materials
Authors: Zhang WX 
Published: February 2021

Time related materials have the advantages of high strength and easy processing. As structural materials, they are more and more widely used in chemical industry, machinery, aerospace, architecture and marine development and other industrial fields. The static and dynamic analysis of these materials and structures under various loading and service conditions has become an important research content in the field of mechanics. Based on the traditional method, this paper presents a simulation technique suitable for solving time-dependent material and structure	problems, and gives the treatment method of boundary conditions.
Mindestens eine von drei Personen weltweit bedarf einer Rehabilitation
Authors: Meyer Thorsten 
Published: February 2021

Liebe Leserinnen, liebe Leser,auch wenn uns die Auswirkungen der Pandemie weiterhin in Atem halten – es lohnt sich auch in diesen Zeiten der Blick auf die längerfristigen Entwicklungstrends in der Rehabilitation. Daher möchte ich gerne neben den Beiträgen dieser aktuellen Ausgabe Ihre Aufmerksamkeit auf zwei für die Rehabilitation international relevante Aktivitäten richten.