bluuebunny/crossref_metadata_2025_split huggingface dataset:
PCA via joint graph Laplacian and sparse constraint: Identification of differentially expressed genes and sample clustering on gene expression data
Authors: Feng Chun-Mei , Xu Yong , Hou Mi-Xiao , Dai Ling-Yun , Shang Jun-Liang 
Published: December 2019

Abstract
Background
In recent years, identification of differentially expressed genes and sample clustering have become hot topics in bioinformatics. Principal Component Analysis (PCA) is a widely used method in gene expression data. However, it has two limitations: first, the geometric structure hidden in data, e.g., pair-wise distance between data points, have not been explored. This information can facilitate sample clustering; second, the Principal Components (PCs) determined by PCA are dense, leading to hard interpretation. However, only a few of genes are related to the cancer. It is of great significance for the early diagnosis and treatment of cancer to identify a handful of the differentially expressed genes and find new cancer biomarkers.

Results
In this study, a new method gLSPCA is proposed to integrate both graph Laplacian and sparse constraint into PCA. gLSPCA on the one hand improves the clustering accuracy by exploring the internal geometric structure of the data, on the other hand identifies differentially expressed genes by imposing a sparsity constraint on the PCs.

Conclusions
Experiments of gLSPCA and its comparison with existing methods, including Z-SPCA, GPower, PathSPCA, SPCArt, gLPCA, are performed on real datasets of both pancreatic cancer (PAAD) and head & neck squamous carcinoma (HNSC). The results demonstrate that gLSPCA is effective in identifying differentially expressed genes and sample clustering. In addition, the applications of gLSPCA on these datasets provide several new clues for the exploration of causative factors of PAAD and HNSC.
Multi-cancer samples clustering via graph regularized low-rank representation method under sparse and symmetric constraints
Authors: Wang Juan , Lu Cong-Hai , Liu Jin-Xing , Dai Ling-Yun , Kong Xiang-Zhen 
Published: December 2019

AbstractBackgroundIdentifying different types of cancer based on gene expression data has become hotspot in bioinformatics research. Clustering cancer gene expression data from multiple cancers to their own class is a significance solution. However, the characteristics of high-dimensional and small samples of gene expression data and the noise of the data make data mining and research difficult. Although there are many effective and feasible methods to deal with this problem, the possibility remains that these methods are flawed.ResultsIn this paper, we propose the graph regularized low-rank representation under symmetric and sparse constraints (sgLRR) method in which we introduce graph regularization based on manifold learning and symmetric sparse constraints into the traditional low-rank representation (LRR). For the sgLRR method, by means of symmetric constraint and sparse constraint, the effect of raw data noise on low-rank representation is alleviated. Further, sgLRR method preserves the important intrinsic local geometrical structures of the raw data by introducing graph regularization. We apply this method to cluster multi-cancer samples based on gene expression data, which improves the clustering quality. First, the gene expression data are decomposed by sgLRR method. And, a lowest rank representation matrix is obtained, which is symmetric and sparse. Then, an affinity matrix is constructed to perform the multi-cancer sample clustering by using a spectral clustering algorithm, i.e., normalized cuts (Ncuts). Finally, the multi-cancer samples clustering is completed.ConclusionsA series of comparative experiments demonstrate that the sgLRR method based on low rank representation has a great advantage and remarkable performance in the clustering of multi-cancer samples.
Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method
Authors: Yao Yu-hua , Lv Ya-ping , Li Ling , Xu Hui-min , Ji Bin-bin , Chen Jing , Li Chun , Liao Bo , Nan Xu-ying 
Published: December 2019

AbstractBackgroundSubcellular localization prediction of protein is an important component of bioinformatics, which has great importance for drug design and other applications. A multitude of computational tools for proteins subcellular location have been developed in the recent decades, however, existing methods differ in the protein sequence representation techniques and classification algorithms adopted.ResultsIn this paper, we firstly introduce two kinds of protein sequences encoding schemes: dipeptide information with space and Gapped k-mer information. Then, the Gapped k-mer calculation method which is based on quad-tree is also introduced.Conclusions>From the prediction results, this method not only reduces the dimension, but also improves the prediction precision of protein subcellular localization.
Clonal reconstruction from time course genomic sequencing data
Authors: Ismail Wazim Mohammed , Tang Haixu 
Published: December 2019

Abstract
Background
Bacterial cells during many replication cycles accumulate spontaneous mutations, which result in the birth of novel clones. As a result of this clonal expansion, an evolving bacterial population has different clonal composition over time, as revealed in the long-term evolution experiments (LTEEs). Accurately inferring the haplotypes of novel clones as well as the clonal frequencies and the clonal evolutionary history in a bacterial population is useful for the characterization of the evolutionary pressure on multiple correlated mutations instead of that on individual mutations.

Results
In this paper, we study the computational problem of reconstructing the haplotypes of bacterial clones from the variant allele frequencies observed from an evolving bacterial population at multiple time points. We formalize the problem using a maximum likelihood function, which is defined under the assumption that mutations occur spontaneously, and thus the likelihood of a mutation occurring in a specific clone is proportional to the frequency of the clone in the population when the mutation occurs. We develop a series of heuristic algorithms to address the maximum likelihood inference, and show through simulation experiments that the algorithms are fast and achieve near optimal accuracy that is practically plausible under the maximum likelihood framework. We also validate our method using experimental data obtained from a recent study on long-term evolution of Escherichia coli.

Conclusion
We developed efficient algorithms to reconstruct the clonal evolution history from time course genomic sequencing data. Our algorithm can also incorporate clonal sequencing data to improve the reconstruction results when they are available. Based on the evaluation on both simulated and experimental sequencing data, our algorithms can achieve satisfactory results on the genome sequencing data from long-term evolution experiments.

Availability
The program (ClonalTREE) is available as open-source software on GitHub at https://github.com/COL-IU/ClonalTREE.
Neuromyelitis optica spectrum disorder with massive basal ganglia involvement: a case report
Authors: Ohara Shinji , Miyahira Taka-aki , Oguchi Kenya , Takei Yo-ichi , Yanagimura Fumihiro , Kawachi Izumi , Oyanagi Kiyomitsu , Kakita Akiyoshi 
Published: December 2019

Abstract
Background
Occurrence of basal ganglia involvement in neuromyelitis optica spectrum disorders (NMOSD) has rarely been reported and none documented pathologically.

Case presentation
A 73-year-old female was clinically diagnosed with a NMOSD based on the clinical and radiological features and positive serum autoantibodies to AQP4. One month before her death, she became acutely ill with disturbed consciousness and right hemiparesis, and was diagnosed and treated as having basal ganglia infarction based on the brain CT. She made a partial recovery but later died from heart failure. At autopsy, the corresponding basal ganglia process revealed a large fresh area of necrosis. Histologically, several pathological signatures of NMOSD could be recognized in the lesion, including inflammatory cell infiltrations by B and T lymphocytes, perivascular complement and fibrinogen deposition, and the appearance of numerous phagocytosed corpora amylacea within the infiltrating macrophages.

Conclusions
The present case illustrates that basal ganglia may be directly involved in the pathological processes of NMOSD, although the possibility of modification of the lesions by superimposed regional ischemia could not be excluded.
Robot-assisted laparoendoscopic single-site surgery for the simultaneous management of multiple urinary tract calculi: a case report and experience sharing
Authors: Zhang Fan , Shan Lisong , Yin Jiahui , Liu Luyang , Wang Pengchao , Sun Shengkun , Zhang Xu , Li Hongzhao , Ma Xin , Guo Gang , Liu Qiming 
Published: December 2019

Abstract
Background
Urolithiasis is a clinically common benign disease in urology. Surgical treatments that are widely used in urolithiasis are percutaneous nephrolithotomy, rigid/flexible ureteroscopy, laparoscopic surgery, and endoscopic combined intrarenal surgery. The da Vinci surgical system is rarely used in the treatment of urolithiasis. In the current study, we report a case of multiple urinary tract calculi treated by robot-assisted laparoendoscopic single-site (RA-LESS) surgery.

Case presentation
A 49-year-old male patient was admitted to our hospital and diagnosed with multiple urinary tract calculi. He previously underwent right ureterolithotomy, laparoscopic cholecystectomy, and extracorporeal shockwave lithotripsy. Computed tomography (CT) scan and three-dimensional reconstruction CT image showed that multiple calculi were located in the right kidney, right upper ureter, and bladder. The preoperative glomerular filtration rate (GFR) were 17.81 ml/min (right kidney) and 53.11 ml/min (left kidney). We utilized the da Vinci system docking with a single-site port to perform pyelolithotomy, ureterolithotomy, and cystolithotomy, simultaneously. The operative time was 135 min and estimated blood loss was 30 ml. The postoperative hospital stay was 5 days. Three months after surgery, the serum creatinine and urea nitrogen levels dropped to a normal range, and no residual fragments were found in the CT scan. The postoperative GFR were 26.33 ml/min (right kidney) and 55.25 ml/min (left kidney).

Conclusions
RA-LESS surgery is a safe and effective surgical procedure in the treatment of multiple urinary tract calculi; however, further investigation is needed to validate its long-term therapeutic effect.
Virus-based pharmaceutical production in plants: an opportunity to reduce health problems in Africa
Authors: Bamogo Pingdwende Kader Aziz , Brugidou Christophe , Sérémé Drissa , Tiendrébéogo Fidèle , Djigma Florencia Wendkuuni , Simpore Jacques , Lacombe Séverine 
Published: December 2019

AbstractBackgroundDeveloping African countries face health problems that they struggle to solve. The major causes of this situation are high therapeutic and logistical costs. Plant-made therapeutics are easy to produce due to the lack of the safety considerations associated with traditional fermenter-based expression platforms, such as mammalian cells. Plant biosystems are easy to scale up and inexpensive, and they do not require refrigeration or a sophisticated medical infrastructure. These advantages provide an opportunity for plant-made pharmaceuticals to counteract diseases for which medicines were previously inaccessible to people in countries with few resources.Main bodyThe techniques needed for plant-based therapeutic production are currently available. Viral expression vectors based on plant viruses have greatly enhanced plant-made therapeutic production and have been exploited to produce a variety of proteins of industrial, pharmaceutical and agribusiness interest. Some neglected tropical diseases occurring exclusively in the developing world have found solutions through plant bioreactor technology. Plant viral expression vectors have been reported in the production of therapeutics against these diseases occurring exclusively in the third world, and some virus-derived antigens produced in plants exhibit appropriate antigenicity and immunogenicity. However, all advances in the use of plants as bioreactors have been made by companies in Europe and America. The developing world is still far from acquiring this technology, although plant viral expression vectors may provide crucial help to overcome neglected diseases.ConclusionToday, interest in these tools is rising, and viral amplicons made in and for Africa are in progress. This review describes the biotechnological advances in the field of plant bioreactors, highlights factors restricting access to this technology by those who need it most and proposes a solution to overcome these limitations.
Clavicle hook plate versus distal clavicle locking plate for Neer type II distal clavicle fractures
Authors: Li Liang , Li Tian-yan , Jiang Peichao , Lin Guizhen , Wu Hongxiao , Han Xiaochuan , Yu Xuezhong 
Published: December 2019

AbstractBackgroundThe purpose of this meta-analysis was to compare clavicle hook plates versus distal clavicle locking plates for the treatment of Neer type II distal clavicle fractures.MethodsPubMed (1996 to January 2019), Embase (1980 to January 2019), Web of Science (1990 to January 2019), the Cochrane Library (January 2019), and the China National Knowledge Infrastructure (January 2019) were systematically searched without language restrictions for literature retrieval. The Constant-Murley shoulder joint function score at 3 and 6 months after the operation and the postoperative complications after the operation (shoulder joint pain, abduction restriction, fracture delay healing, subacromial impingement) were the outcomes. Stata 12.0 was used for the meta-analysis.ResultsA total of 9 clinical trials involving 446 patients were finally included in this meta-analysis. The results showed that the improvement in the Constant-Murley shoulder joint function score in the distal locking plate group was better than that in the clavicle hook plate group at 3 and 6 months after the operation (P < 0.05). There were fewer cases of shoulder joint pain and restricted shoulder abduction range of motion in the distal locking plate group, and the difference was statistically significant (P < 0.05). There were no statistically significant differences in fracture delay healing and subacromial impingement between the two groups (P > 0.05).ConclusionCompared with the clavicular hook plate, the distal clavicle locking plate for the treatment of Neer type II distal clavicle fractures is associated with better shoulder function recovery and fewer complications related to pain and abduction restriction.
Overstuffing in resurfacing hemiarthroplasty is a potential risk for failure
Authors: Geervliet Pieter C. , Willems Jore H. , Sierevelt Inger N. , Visser Cornelis P. J. , van Noort Arthur 
Published: December 2019

Abstract
Purpose
Literature describes the concern of an overstuffed shoulder joint after a resurfacing humeral head implant (RHHI). The purpose of this study was to evaluate inter-observer variability of (1) the critical shoulder angle (CSA), (2) the length of the gleno-humeral offset (LGHO), and (3) the anatomic center of rotation (COR) in a patient population operated with a Global Conservative Anatomic Prosthesis (CAP) RHHI. The measurements were compared between the revision and non-revision groups to find predictive indicators for failure.

Methods
Pre- and postoperative radiographs were retrieved from 48 patients who underwent RHHI from 2007 to 2009 using a Global CAP hemiarthroplasty for end-stage osteoarthritis. This cohort consisted of 36 females (12 men) with a mean age of 77 years (SD 7.5). Two musculoskeletal radiologist and two specialized shoulder orthopedic surgeons measured the CSA, LGHO, and COR of all patients.

Results
The inter-observer reliability showed excellent reliability for the CSA, LGHO, and the COR, varying between 0.91 and 0.98. The mean COR of the non-revision group was 4.9 mm (SD 2.5) compared to mean COR of the revision group, 8 mm (SD 2.2) (p < 0.01). The COR is the predictor of failure (OR 1.90 (95%Cl 1.19–3.02)) with a cut of point of 5.8 mm. The mean CSA was 29.8° (SD 3.9) There was no significant difference between the revision and non-revision groups (p = 0.34). The mean LGHO was 2.6 mm (SD 3.3) post-surgery. The mean LGHO of the revision group was 3.9 (SD 1.7) (p = 0.04) post-surgery. Despite the difference in mean LGHO, this is not a predictor for failure.

Conclusion
The CSA, LGHO, and COR can be used on radiographs and have a high inter-observer agreement. In contrast with the CSA and LGHO, we found a correlation between clinical failure and revision surgery in case of a deviation of the COR greater than 5 mm.

Trial registration
Institutional review board, number: ACLU 2016.0054, Ethical Committee number: CBP M1330348. Registered 7 November 2006.
The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (Fundulus heteroclitus)
Authors: Bisese Eleanor C. , Ciuba Chandler M. , Davidson Amelia L. , Kaushik Akanksha , Mullen Sabrina M. , Barth Jeremy L. , Hazard E. Starr , Wilson Robert C. , Hardiman Gary , Hollis David M. 
Published: December 2019

AbstractAdult fish produce new cells throughout their central nervous system during the course of their lives and maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in adult fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received little attention. We sought to examine differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion to the midbrain/diencephalon and examined differentially expressed genes (DEGs) at an acute recovery time of 1 h post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified 404 DEGs with the vast majority being upregulated. Using qPCR, we validated the upregulation of DEGs pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes involved in the injury response of a brain regenerative-capable vertebrate.
Pseudo-Wellens syndrome, acute pancreatitis, and an anomalous coronary artery: a case report
Authors: Effoe V. S. , O’Neal W. , Santos R. , Rubinsztain L. , Zafari A. M. 
Published: December 2019

Abstract
Background
Chest pain associated with transient electrocardiogram changes mimicking an acute myocardial infarction have been described in acute pancreatitis. These ischemic electrocardiogram changes can present a diagnostic dilemma, especially when patients present with concurrent angina pectoris and epigastric pain warranting noninvasive or invasive imaging studies.

Case presentation
A 45-year-old African-American man with a history of alcohol use disorder presented to the emergency department of our institution with 36 hours of concurrent epigastric pain and left-sided chest pain radiating to his left arm and associated with nausea and dyspnea. On physical examination, he was afebrile; his blood pressure was elevated; and he had epigastric tenderness. His laboratory test results were significant for hypokalemia, normal troponin, and elevated serum lipase and amylase levels. Serial electrocardiograms for persistent chest pain showed ST-segment elevations with dynamic T-wave changes in the right precordial electrocardiogram leads, consistent with Wellens syndrome. He was immediately taken to the cardiac catheterization laboratory, where selective coronary angiography showed normal coronary arteries with an anomalous origin of the right coronary artery from the opposite sinus. Given his elevated lipase and amylase levels, the patient was treated for acute alcohol-induced pancreatitis with intravenous fluids and pain control. His chest pain and ischemic electrocardiogram changes resolved within 24 hours of admission, and coronary computed tomography angiography showed an interarterial course of the right coronary artery without high-risk features.

Conclusions
Clinicians may consider deferring immediate cardiac catheterization and attribute electrocardiogram changes to acute pancreatitis in patients presenting with angina pectoris and acute pancreatitis if confirmed by normal cardiac enzymes and elevated levels of lipase and amylase. However, when clinical signs and electrocardiogram findings are highly suggestive of myocardial ischemia/injury, immediate noninvasive coronary computed tomography angiography may be the best approach to make an early diagnosis.
Characteristics of vegetation succession on the Pinus thunbergii forests in warm temperate regions, Jeju Island, South Korea
Authors: Hong Yongsik , Kim Euijoo , Lee Eungpill , Lee Seungyeon , Cho Kyutae , Lee Youngkeun , Chung Sanghoon , Jeong Heonmo , You Younghan 
Published: December 2019

AbstractBackgroundTo investigate the trends of succession occurring at thePinus thunbergiiforests on the lowlands of Jeju Island, we quantified the species compositions and the importance values by vegetation layers of Braun-Blanquet method on thePinus thunbergiiforests. We used multivariate analysis technique to know the correlations between the vegetation group types and the location environmental factors; we used the location environment factors such as altitudes above sea level, tidal winds (distance from the coast), annual average temperatures, and forest gaps to know the vegetation distribution patterns.ResultsAccording to the results on the lowland of Jeju Island, the understory vegetation of the lowlandPinus thunbergiiforests was dominated by tall evergreen broad-leaved trees such asMachilus thunbergii,Neolitsea sericea, andCinnamomum japonicumshowing a vegetation group structure of the mid-succession, and the distribution patterns of vegetation were determined by the altitudes above sea level, the tidal winds on the distance from the coast, the annual average temperatures, and the forest gaps. We could discriminate the secondary succession characteristics of thePinus thunbergiiforests on the lowland and highland of Jeju Island of South Korea.ConclusionsIn the lowland of Jeju Island, the secondary succession will progress to the form ofPinus thunbergii(early successional species)→Machilus thunbergii,Litsea japonica(mid-successional species)→Machilus thunbergii(late-successional species) sequence in the temperate areas with strong tidal winds. In the highland of Jeju Island, the succession will progress to the form ofPinus thunbergii(early successional species)→Neolitsea sericea,Eurya japonica(mid-successional species)→Castanopsis sieboldii(late-successional species) sequence in the areas where tidal winds are weak and temperatures are relatively low. However, local differences between lowland and highland of Jeju Island will be caused by the micro-environmental factors resulting from the topographic differences and the supply of tree seeds. From the characteristics of succession study, we could properly predict and manage thePinus thunbergiiforest ecosystem on lowland and highland of Jeju Island.