bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of serum tRF-23-Q99P9P9NDD as a potential biomarker for the clinical diagnosis of gastric cancer
Authors: Zhang Yu , Gu Xinliang , Qin Xinyue , Huang Yuejiao , Ju Shaoqing 
Published: June 2022

AbstractBackgroundGastric cancer (GC) is one of the diseases that endanger human health with high morbidity and mortality. The positive rates of traditional biomarkers in the diagnosis of GC are low, so it is necessary to find biomarkers with high sensitivity to increase the detection rate. tRNA-derived small RNAs (tsRNAs) are novel small non-coding RNAs with specific biological functions and aberrant expression in cancer. In this study, we focused on the potential of tRNA-derived small RNAs as GC biomarkers.MethodsThe differentially expressed tsRNAs in three pairs of GC tissues were screened with high-throughput sequencing and verified using the TCGA database and Quantitative real-time PCR. The methodological evaluation of tRF-23-Q99P9P9NDD was verified by agarose gel electrophoresis, RIN evaluation, and Sanger sequencing. The Chi-square test was used to evaluate the relationship between the tRF-23-Q99P9P9NDD expression and clinicopathological parameters. Kaplan–Meier survival analysis was used to evaluate the effect of the tRF-23-Q99P9P9NDD expression on survival. Additionally, the receiver operating characteristic curve (ROC) was used to evaluate the diagnostic efficacy of tRF-23-Q99P9P9NDD in GC.ResultsDifferential expression of serum tRF-23-Q99P9P9NDD could distinguish GC patients from gastritis patients and healthy donors. Chi-square test showed that high expression of tRF-23-Q99P9P9NDD was significantly associated with T stage, lymph node metastasis, TNM stage, and nerve/vascular invasion. Kaplan–Meier curve showed that patients with high expression of tRF-23-Q99P9P9NDD had a lower survival rate than patients with low expression of this biomarker. ROC analysis showed that, compared with conventional biomarkers, the efficacy of tRF-23-Q99P9P9NDD was higher, which was improved by the combination of biomarkers, and even in the early stages. Finally, we preliminarily predicted the downstream of tRF-23-Q99P9P9NDD in GC cells.ConclusionsThe expression of tRF-23-Q99P9P9NDD in GC serum can identify GC patients, and it has higher efficacy than conventional biomarkers even in the early stages. Furthermore, tRF-23-Q99P9P9NDD can monitor the postoperative conditions of GC patients.
A Fuzzy-based Sliding Mode Control Approach for Acceleration Slip Regulation of Battery Electric Vehicle
Authors: Shi Qin , Wang Mingwei , He Zejia , Yao Cheng , Wei Yujiang , He Lin 
Published: June 2022

AbstractDue to quick response and large quantity of electric motor torque, the traction wheels of battery electric vehicle are easy to slip during the initial phase of starting. In this paper, a sliding mode control approach of acceleration slip regulation is designed to prevent the slip of the traction wheels. The wheel slip ratio is used as the state variable for the formulation of system dynamics model. The fuzzy algorithm is utilized to adjust the switch function of sliding mode controller. After stability and robustness analysis, the sliding mode control law is transferred into C code and downloaded into vehicle control unit, which is validated under wet and dry road conditions. The experimental results with a small overshoot and a quick response during starting indicate that the sliding mode controller has good control effect on the slip ratio regulation. This article proposes an acceleration slip regulation method that improves the safety during acceleration for battery electric vehicle.
Movement Modeling and Control for Robotic Bonnet Polishing
Authors: Huang Xuepeng , Wang Zhenzhong , Lin Zewen 
Published: June 2022

AbstractWith the increasing demand for high-precision optical components, bonnet polishing technology is increasingly being used in the polishing process of optical components owing to its high removal efficiency and high surface accuracy. However, it is expensive and difficult to implement dedicated bonnet polishing machine tools, and their processing range is limited. This research combines bonnet polishing technology with industrial robot-assisted processing technology to propose a robotic bonnet polishing control model for large-diameter axisymmetric aspherical optical components. Using the transformation relations of the spatial coordinate system, the transformation relations of the workpiece coordinate system, local coordinate system of the polishing point, and tool coordinate system of the bonnet sphere center are established to obtain the bonnet precession polishing motion model. The polishing trajectory of large-diameter axisymmetric aspherical components and the variation in the linkage angle difference were simulated by adding an efficiency-optimal control strategy to the motion model. The robot motion was simulated in Robostudio to verify the correctness of the precession motion model and control algorithm. Lastly, the robotic bonnet polishing system was successfully applied to the polishing process of the optical components.
Experimental study of compressive properties parallel to grain of glulam
Authors: Totsuka Marina , Jockwer Robert , Kawahara Hiro , Aoki Kenji , Inayama Masahiro 
Published: June 2022

AbstractThis paper describes results and analysis of experiment of compression behavior parallel to grain of glulam (Norway Spruce, Japanese cedar, and Japanese cypress), especially in damage zones near loading plates and joints. To investigate the influence factors of physical properties and the mechanism of the damage zone near the loading plates or the joints, compression tests on 90 specimens and surface-measurement tests on 48 specimens were performed. As a result, it was observed that damage zones existed near the loading plates and the joints. The lengths of the damage zone of wood–wood joints are larger than that of wood–steel joints. The length of the damage zone was independent of the load and the height of the specimens. However, the length of the damage zone and its scatter increase as the width of the cross-section increases, as does the roughness on the contact surface. It was considered that the cause of the damage zone is the roughness on the contact surface and the length of the damage zone depends on the roughness on the contact surface. Therefore, the length of the damage zone depends on the processing accuracy on the contact surface and has an increasing trend as the contact-surface area increases. There was the size effect of the height of the specimens on the compressive strength because of knots.
Improving durability of cross laminated timber (CLT) with borate treatment
Authors: Bagheri Sajad , Alinejad Mona , Ohno Katie , Hasburgh Laura , Arango Rachel , Nejad Mojgan 
Published: June 2022

AbstractBorate solution was used to treat two sets of Douglas-fir wood samples, one by spraying cross-laminated timbers (CLT) and another set by dip-treating wood in solutions at different retentions. A novel model was developed to explain and predict borate uptake based on dip-treatment parameters. Small-scale CLT samples were prepared using commercial emulsion polymer isocyanate (EPI) and polyurethane (PU) adhesive with dip-treated wood. The effect of adhesive and borate retention on CLT samples were evaluated through adhesion, fire, termite, and decay tests. The adhesion strength of wood was statistically unaffected by borate treatment. Statistical analysis showed that both spray- and dip-treated samples had significantly higher termite and decay resistance and fire performance than the untreated boards. Untreated CLT samples bonded with PU showed a considerably higher inherent decay and termite resistance than untreated specimens bonded with EPI adhesive.
Reversely immortalized mouse salivary gland cells presented a promising metabolic and fibrotic response upon BMP9/Gdf2 stimulation
Authors: Luo Wenping , Liang Panpan , Zhao Tianyu , Cheng Qianyu , Liu Huikai , He Liwen , Zhang Linghuan , Huang Bo , Zhang Yuxin , He Tongchuan , Yang Deqin 
Published: June 2022

AbstractThe submandibular gland (SMG) and the sublingual gland (SLG) are two of the three major salivary glands in mammals. In mice, they are adjacent to each other and open into the oral cavity, producing saliva to lubricate the mouth and aid in food digestion. Though salivary gland dysfunction accompanied with fibrosis and metabolic disturbance is common in clinic, in-depth mechanistic research is lacking. Currently, research on how to rescue salivary function is challenging, as it must resort to using terminally differentiated acinar cells or precursor acinar cells with unknown differentiation. In this study, we established reversely immortalized mouse primary SMG cells (iSMGCs) and SLG cells (iSLGCs) on the first postnatal day (P0). The iSMGCs and iSLGCs grew well, exhibited many salivary gland characteristics, and retained the metabolism-related genes derived from the original tissue as demonstrated using transcriptome sequencing (RNA-seq) analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these two cell lines, which overlapped with those of the SMG and SLG, were enriched in cysteine and methionine metabolism. Furthermore, we investigated the role of bone morphogenetic protein 9 (BMP9), also known as growth differentiation factor 2(Gdf2), on metabolic and fibrotic functions in the SMG and SLG. We demonstrated that iSMGCs and iSLGCs presented promising adipogenic and fibrotic responses upon BMP9/Gdf2stimulation. Thus, our findings indicate that iSMGCs and iSLGCs faithfully reproduce characteristics of SMG and SLG cells and present a promising prospect for use in future study of salivary gland metabolism and fibrosis upon BMP9/Gdf2stimulation.
Alpha-smooth muscle actin-positive cancer-associated fibroblasts secreting osteopontin promote growth of luminal breast cancer
Authors: Muchlińska Anna , Nagel Anna , Popęda Marta , Szade Jolanta , Niemira Magdalena , Zieliński Jacek , Skokowski Jarosław , Bednarz-Knoll Natalia , Żaczek Anna J. 
Published: June 2022

Abstract
Background
Cancer-associated fibroblasts (CAFs) have been shown to support tumor development in a variety of cancers. Different markers were applied to classify CAFs in order to elucidate their impact on tumor progression. However, the exact mechanism by which CAFs enhance cancer development and metastasis is yet unknown.

Methods
Alpha-smooth muscle actin (α-SMA) was examined immunohistochemically in intratumoral CAFs of nonmetastatic breast cancers and correlated with clinicopathological data. Four CAF cell lines were isolated from patients with luminal breast cancer (lumBC) and classified according to the presence of α-SMA protein. Conditioned medium (CM) from CAF cultures was used to assess the influence of CAFs on lumBC cell lines: MCF7 and T47D cells using Matrigel 3D culture assay. To identify potential factors accounting for promotion of tumor growth by α-SMAhigh CAFs, nCounter PanCancer Immune Profiling Panel (NanoString) was used.

Results
In luminal breast cancer, presence of intratumoral CAFs expressing high level of α-SMA (13% of lumBC group) correlated with poor prognosis (p = 0.019). In in vitro conditions, conditioned medium obtained from primary cultures of α-SMA-positive CAFs isolated from luminal tumors was observed to enhance growth of lumBC cell line colonies in 3D Matrigel, in contrast to CM derived from α-SMA-negative CAFs. Multigene expression analysis indicated that osteopontin (OPN) was overexpressed in α-SMA-positive CAFs in both clinical samples and in vitro models. OPN expression was associated with higher percentage of Ki67-positive cells in clinical material (p = 0.012), while OPN blocking in α-SMA-positive CAF-derived CM attenuated growth of lumBC cell line colonies in 3D Matrigel.

Conclusions
Our findings demonstrate that α-SMA-positive CAFs might enhance tumor growth via secretion of OPN.
The importance of deep speech phenotyping for neurodevelopmental and genetic disorders: a conceptual review
Authors: Chenausky Karen V. , Tager-Flusberg Helen 
Published: June 2022

AbstractBackgroundSpeech is the most common modality through which language is communicated, and delayed, disordered, or absent speech production is a hallmark of many neurodevelopmental and genetic disorders. Yet, speech is not often carefully phenotyped in neurodevelopmental disorders. In this paper, we argue that such deep phenotyping, defined as phenotyping that is specific to speech production and not conflated with language or cognitive ability, is vital if we are to understand how genetic variations affect the brain regions that are associated with spoken language.Speech is distinct from language, though the two are related behaviorally and share neural substrates. We present a brief taxonomy of developmental speech production disorders, with particular emphasis on the motor speech disorders childhood apraxia of speech (a disorder of motor planning) and childhood dysarthria (a set of disorders of motor execution). We review the history of discoveries concerning the KE family, in whom a hereditary form of communication impairment was identified as childhood apraxia of speech and linked to dysfunction in theFOXP2gene. The story demonstrates how instrumental deep phenotyping of speech production was in this seminal discovery in the genetics of speech and language. There is considerable overlap between the neural substrates associated with speech production and withFOXP2expression, suggesting that further genes associated with speech dysfunction will also be expressed in similar brain regions. We then show how a biologically accurate computational model of speech production, in combination with detailed information about speech production in children with developmental disorders, can generate testable hypotheses about the nature, genetics, and neurology of speech disorders.ConclusionsThough speech and language are distinct, specific types of developmental speech disorder are associated with far-reaching effects on verbal communication in children with neurodevelopmental disorders. Therefore, detailed speech phenotyping, in collaboration with experts on pediatric speech development and disorders, can lead us to a new generation of discoveries about how speech development is affected in genetic disorders.
The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts
Authors: Hasan Sharmin , Huang Lichun , Liu Qiaoquan , Perlo Virginie , O’Keeffe Angela , Margarido Gabriel Rodrigues Alves , Furtado Agnelo , Henry Robert J. 
Published: June 2022

Abstract
Background
High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome.

Results
A cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel.

Conclusion
The data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.
Primary small cell carcinoma of the ureter with associated hyponatremia and rapid progression to bladder involvement: a case report
Authors: Chuang Yu-Hsiang , Nandwani Ghulam Mustafa , Szewczyk-Bieda Magdelena , Kernohan Neil , Aslam Muhammad Zeeshan 
Published: June 2022

Abstract
Background
Primary small cell carcinoma (SmCCa) of the ureter is rare. The majority of patients present with visible haematuria. Diagnosis is confirmed by histopathology. Associated hyponatraemia in GU lesion can be due SmCCa can be useful for early diagnosis aggressive ureteric tumors. The current management includes radical surgery or radiotherapy with concomitant chemotherapy to improve survival and quality of life.

Case presentation
We present a case of a 77 years female who was found to have unilateral hydronephrosis with a 5 cm filling defect in the distal ureter on CT urogram. Further staging showed organ-confined disease. Serum sodium levels were low at presentation. At the time of planned nephroureterectomy (NU), cystoscopy revealed a bladder tumor obstructing the right ureteric orifice. TURBT was performed instead. After TURBT, there was marked hyponatremia and histology was small cell carcinoma (SmCCa). Paraneoplastic SIADH was the likely cause. Neoadjuvant chemotherapy (NACT) followed by radiotherapy (RT) was chosen for definitive treatment. This resulted in an excellent response supported by radiological evidence of almost complete resolution of the tumor.

Conclusion
The presence of genitourinary lesion and hyponatremia should raise suspicion of paraneoplastic SIADH. The case suggests the emphasis of histological diagnosis of the genitourinary lesion with existing hyponatraemia to provide better outcome with NACT followed by definitive treatment. We share our experience of NACT and RT in the management of ureteric SmCCa extension to the bladder.
The association between long-term night shift work and metabolic syndrome: a cross-sectional study of male railway workers in southwest China
Authors: Dong Chaohui , Zeng Honglian , Yang Bo , Zhang Yi , Li Zhitao 
Published: June 2022

Abstract
Objectives
Metabolic syndrome (MetS) increases the risk of new diabetes and cardiovascular disease. Night shift work (NSW) may influence metabolic disturbance and lead to MetS. This study aims to investigate the association between long-term NSW (≥ 10 years) and MetS combined with its components in male railway workers in southwest China.

Methods
11,023 male railway workers with long-term NSW of more than 10 years in the Physical Examination Center of the Affiliated Hospital of Chengdu University were enrolled. The basic data were collected by investigators and blood test results were collected. The primary outcome was the prevalence of metabolic syndrome. The results were analyzed using statistical software SPSS 22.0.

Results
In total, 11,023 people over the age of 40 with more than 10 years of working experience were enrolled, and 4759 (43.2%) participants had a diagnosis of MetS. The basic data indicated that night shift workers tended to be younger, shorter working years, but with higher body mass index and longer hip circumference (p < 0.05). The adjusted analysis revealed that there was no significant association between NSW and metabolic syndrome (OR 1.03, 95% CI 0.94–1.12, p = 0.543). NSW was associated with SBP ≥ 130 mmHg (OR 1.11, 95% CI 1.02–1.21, p < 0.001) and waist circumference ≥ 90 cm (OR 1.11, 95% CI 1.02–1.21, p < 0.001).

Conclusions
Long-term night shift workers had a higher prevalence of MetS. However, long-term NSW is not associated with a significantly increased risk of metabolic syndrome in male railway workers in southwest China. Long-term NSW is associated with elevated SBP, and waist circumference increase.
On estimation for accelerated failure time models with small or rare event survival data
Authors: Alam Tasneem Fatima , Rahman M. Shafiqur , Bari Wasimul 
Published: June 2022

AbstractBackgroundSeparation or monotone likelihood may exist in fitting process of the accelerated failure time (AFT) model using maximum likelihood approach when sample size is small and/or rate of censoring is high (rare event) or there is at least one strong covariate in the model, resulting in infinite estimates of at least one regression coefficient.MethodsThis paper investigated the properties of the maximum likelihood estimator (MLE) of the regression parameters of the AFT models for small sample and/or rare-event situation and addressed the problems by introducing a penalized likelihood approach. The penalized likelihood function and the corresponding score equation is derived by adding a penalty term to the existing likelihood function, which was originally proposed by Firth (Biometrika, 1993) for the exponential family models. Further, a post-hoc adjustment of intercept and scale parameters is discussed keeping them out of penalization to ensure accurate prediction of survival probability. The penalized method was illustrated for the widely used log-location-scale family models such as Weibull, Log-normal and Log-logistic distributions and compared the models and methods uisng an extensive simulation study.ResultsThe simulation study, performed separately for each of the log-location-scale models, showed that Firth’s penalized likelihood succeeded to solve the problem of separation and achieve convergence, providing finite estimates of the regression coefficients, which are not often possible by the MLE. Furthermore, the proposed penalized method showed substantial improvement over MLE by providing smaller amount of bias, mean squared error (MSE), narrower confidence interval and reasonably accurate prediction of survival probabilities. The methods are illustrated using prostate cancer data with existence of separation, and results supported the simulation findings.ConclusionWhen sample size is small (≤ 50) or event is rare (i.e., censoring proportion is high) and/or there is any evidence of separation in the data, we recommend to use Firth’s penalized likelihood method for fitting AFT model.