bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Structure of Nation-Wide Rice in Thailand
Authors: Vejchasarn Phanchita , Shearman Jeremy R. , Chaiprom Usawadee , Phansenee Yotwarit , Suthanthangjai Arissara , Jairin Jirapong , Chamarerk Varapong , Tulyananda Tatpong , Amornbunchornvej Chainarong 
Published: October 2021

Abstract
Background
Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.

Results
The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure.

Conclusion
The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.
Overexpression of OsLCT2, a Low-Affinity Cation Transporter Gene, Reduces Cadmium Accumulation in Shoots and Grains of Rice
Authors: Tang Li , Dong Jiayu , Tan Longtao , Ji Zhongying , Li Yaokui , Sun Yuantao , Chen Caiyan , Lv Qiming , Mao Bigang , Hu Yuanyi , Zhao Bingran 
Published: October 2021

AbstractCadmium (Cd)-contaminated rice is a serious issue affecting food safety. Understanding the molecular regulatory mechanisms of Cd accumulation in rice grains is crucial to minimizing Cd concentrations in grains. We identified a member of the low-affinity cation transporter family, OsLCT2 in rice. It was a membrane protein. OsLCT2 was expressed in all tissues of the elongation and maturation zones in roots, with the strongest expression in pericycle and stele cells adjacent to the xylem. When grown in Cd-contaminated paddy soils, rice plants overexpressing OsLCT2 significantly reduced Cd concentrations in the straw and grains. Hydroponic experiment demonstrated its overexpression decreased the rate of Cd translocation from roots to shoots, and reduced Cd concentrations in xylem sap and in shoots of rice. Moreover, its overexpression increased Zn concentrations in roots by up-regulating the expression of OsZIP9, a gene responsible for Zn uptake. Overexpression of OsLCT2 reduces Cd accumulation in rice shoots and grains by limiting the amounts of Cd loaded into the xylem and restricting Cd translocation from roots to shoots of rice. Thus, OsLCT2 is a promising genetic resource to be engineered to reduce Cd accumulation in rice grains.
Multi-scale Monte Carlo simulations of gold nanoparticle-induced DNA damages for kilovoltage X-ray irradiation in a xenograft mouse model using TOPAS-nBio
Authors: Klapproth Alexander P. , Schuemann Jan , Stangl Stefan , Xie Tianwu , Li Wei Bo , Multhoff Gabriele 
Published: October 2021

Abstract
Background
Gold nanoparticles (AuNPs) are considered as promising agents to increase the radiosensitivity of tumor cells. However, the biological mechanisms of radiation enhancement effects of AuNPs are still not well understood. We present a multi-scale Monte Carlo simulation framework within TOPAS-nBio to investigate the increase of DNA damage due to the presence of AuNPs in mouse tumor models.

Methods
A tumor was placed inside a voxel mouse model and irradiated with either 100-kVp or 200-kVp X-ray beams. Phase spaces were employed to transfer particles from the macroscopic (voxel) scale to the microscopic scale, which consists of a cell geometry including a detailed mouse DNA model. Radiosensitizing effects were calculated in the presence and absence of hybrid nanoparticles with a $$\text{Fe}_2\text{O}_3$$

Fe
2

O
3

core surrounded by a gold layer (AuFeNPs). To simulate DNA damage even for very small energy tracks, Geant4-DNA physics and chemistry models were used on microscopic scale.

Results
An AuFeNP-induced enhancement of both dose and DNA strand breaks has been established for different scenarios. Produced chemical radicals including hydroxyl molecules, which were assumed to be responsible for DNA damage through chemical reactions, were found to be significantly increased. We further observed a dependency of the results on the location of the cells within the tumor for 200-kVp X-ray beams.

Conclusion
Our multi-scale approach allows to study irradiation-induced physical and chemical effects on cells. We showed a potential increase in cell radiosensitization caused by relatively small concentrations of AuFeNPs. Our new methodology allows the individual adjustment of parameters in each simulation step and therefore can be used for other studies investigating the radiosensitizing effects of AuFeNPs or AuNPs in living cells.
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery
Authors: Liu Yusong , Ye Xiufen , Yu Christina Y. , Shao Wei , Hou Jie , Feng Weixing , Zhang Jie , Huang Kun 
Published: October 2021

Abstract
Background
Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. However, these algorithms have limitations such as insufficient granularity and unbalanced module size, which prevent full acquisition of knowledge from data mining. In addition, it is difficult to incorporate prior knowledge in current co-expression module detection algorithms.

Results
In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. In addition, the proposed algorithm can identify modules by incorporating prior knowledge.

Conclusion
In summary, we developed a method to obtain as much as possible information from networks with increased input coverage and the ability to detect more size-balanced and granular modules. In addition, our method can integrate data from different sources. Our proposed method performs better than current methods with complete coverage of input genes and finer granularity. Moreover, this method is designed not only for gene co-expression networks but can also be applied to any general fully connected weighted network.
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process
Authors: Maiolo Massimo , Gatti Lorenzo , Frei Diego , Leidi Tiziano , Gil Manuel , Anisimova Maria 
Published: October 2021

Abstract
Background
Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences.

Results
We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license.

Conclusions
The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns.
An Ensemble Deep Learning based Predictor for Simultaneously Identifying Protein Ubiquitylation and SUMOylation Sites
Authors: He Fei , Li Jingyi , Wang Rui , Zhao Xiaowei , Han Ye 
Published: October 2021

Abstract
Background
Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, existing methods generally rely on feature engineering, and ignore the natural similarity between the two types of protein translational modification. This study is the first all-in-one deep network to predict protein Ubiquitylation and SUMOylation sites from protein sequences as well as their crosstalk sites simultaneously. Our deep learning architecture integrates several meta classifiers that apply deep neural networks to protein sequence information and physico-chemical properties, which were trained on multi-label classification mode for simultaneously identifying protein Ubiquitylation and SUMOylation as well as their crosstalk sites.

Results
The promising AUCs of our method on Ubiquitylation, SUMOylation and crosstalk sites achieved 0.838, 0.888, and 0.862 respectively on tenfold cross-validation. The corresponding APs reached 0.683, 0.804 and 0.552, which also validated our effectiveness.

Conclusions
The proposed architecture managed to classify ubiquitylated and SUMOylated lysine residues along with their crosstalk sites, and outperformed other well-known Ubiquitylation and SUMOylation site prediction tools.
Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change
Authors: Song Kai , Gao Bin , Halvarsson Peter , Fang Yun , Klaus Siegfried , Jiang Ying-Xin , Swenson Jon E. , Sun Yue-Hua , Höglund Jacob 
Published: October 2021

Abstract
Background
The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China.

Results
We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes.

Conclusions
Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.
Endoscopic ultrasound guided fine needle biopsy (EUS-FNB) from peritoneal lesions: a prospective cohort pilot study
Authors: Kongkam Pradermchai , Orprayoon Theerapat , Yooprasert Sirilak , Sirisub Nakarin , Klaikaew Naruemon , Sanpawat Anapat , Safa Shahram , Ridtitid Wiriyaporn , Kullavanijaya Pinit , Rerknimitr Rungsun 
Published: October 2021

Abstract
Background
Diagnostic laparoscopy is often a necessary, albeit invasive, procedure to help resolve undiagnosed peritoneal diseases. Previous retrospective studies reported that EUS-FNA is feasible on peritoneal and omental lesions, however, EUS-FNA provided a limited amount of tissue for immunohistochemistry stain (IHC).

Aim
This pilot study aims to prospectively determine the effectiveness of EUS-FNB regarding adequacy of tissue for IHC staining, diagnostic rate and the avoidance rate of diagnostic laparoscopy or percutaneous biopsy in patients with these lesions.

Methods
From March 2017 to June 2018, patients with peritoneal or omental lesions identified by CT or MRI at the King Chulalongkorn Memorial Hospital, Bangkok, Thailand were prospectively enrolled in the study. All Patients underwent EUS-FNB. For those with negative pathological results of EUS-FNB, percutaneous biopsy or diagnostic laparoscopy was planned. Analysis uses percentages only due to small sample sizes.

Results
A total of 30 EUS-FNB passes were completed, with a median of 3 passes (range 2–3 passes) per case. For EUS-FNB, the sensitivity, specificity, PPV, NPV and accuracy of EUS-FNB from peritoneal lesions were 63.6%, 100%, 100%, 20% and 66.7% respectively. Adequate tissue for IHC stain was found in 25/30 passes (80%). The tissues from EUS results were found malignant in 7/12 patients (58.3%). IHC could be done in 10/12 patients (83.3%). Among the five patients with negative EUS results, two underwent either liver biopsy of mass or abdominal paracentesis, showing gallbladder cancer and adenocarcinoma. Two patients refused laparoscopy due to advanced pancreatic cancer and worsening ovarian cancer. The fifth patient had post-surgical inflammation only with spontaneous resolution. The avoidance rate of laparoscopic diagnosis was 58.3%. No major adverse event was observed.

Conclusions
EUS-FNB from peritoneal lesions provided sufficient core tissue for diagnosis and IHC. Diagnostic laparoscopy can often be avoided in patients with peritoneal lesions.
A rare case of severe gastroenteritis caused by Aeromonas hydrophila after colectomy in a patient with anti-Hu syndrome: a case report
Authors: Greiner Michael , Anagnostopoulos Alexia , Pohl Daniel , Zbinden Reinhard , Zbinden Andrea 
Published: October 2021

Abstract
Background
Aeromonas hydrophila is a gram-negative facultative anaerobic coccobacillus, which is an environmental opportunistic pathogen. A. hydrophila are involved in several infectious diseases such as gastroenteritis, septicemia and wound infections. However, gastroenteritis caused by Aeromonas spp. are rare and the clinical relevance of Aeromonas species in stool specimens is still under debate.

Case presentation
Our case concerns a 32-year-old woman who presented at hospital with a worsening watery diarrhea and fever requiring intensive care. A cholera-like illness was diagnosed. The patient had a past history of an anti-Hu syndrome with a myenteric ganglionitis. A molecular multiplex RT-PCR (QIAstat-Dx Gastrointestinal Panel, QIAGEN) covering a broad spectrum of diverse gastrointestinal pathogens performed directly from the stool was negative but the stool culture revealed growth of A. hydrophila. Further investigations of the A. hydrophila strain in cell cultures revealed the presence of a cytotoxic enterotoxin.

Conclusions
Although A. hydrophila rarely causes gastroenteritis, Aeromonas spp. should be considered as a causative agent of severe gastroenteritis with a cholera-like presentation. This case highlights the need to perform culture methods from stool samples when PCR-based methods are negative and gastrointestinal infection is suspected.
A case report of community-acquired Raoultella ornithinolytica infection in a healthy, young individual
Authors: Chen Xiaonan , Zhou Xinjian , Cao Jun , Ma Ke , Xia Zhijie 
Published: October 2021

Abstract
Background
Raoultella ornithinolytica is a Gram-negative bacillus that resembles Klebsiella. This bacterium is present in many soil and aquatic environments and is a major causative agent of healthcare-associated infections (HAIs) in medical staff. Clinically, it has been reported to contribute to nosocomial infections in patients that include but are not limited to gastrointestinal, skin, and genitourinary tract infections. These complications are most common in hospitalized patients with underlying immunodeficiency, multiple comorbidities, or those receiving invasive surgery.

Case presentation
We present a case of a 25-year-old patient with a R. ornithinolytica infection. The patient had no history of any disease. Her main complaints were high fever, a scattered maculopapular rash, and superficial lymph node enlargement (SLNE). Peripheral blood samples were collected for high-throughput sequencing analysis to identify pathogenic microorganisms. The results confirmed a R. ornithinolytica infection, which was treated successfully using meropenem. Loratadine was also administered to treat the patient’s compromised skin condition caused by an allergic reaction.

Conclusions
To our knowledge, this is the first case of a systemic maculopapular rash and superficial lymphadenopathy caused by a R. ornithinolytica infection acquired at the community level. Based on this case, we recommend a combination of antibiotic and antiallergic drugs to treat a R. ornithinolytica infection and associated allergic reaction to the bacteria.
Intersecting systemic and personal barriers to accessing social services: qualitative interviews in northern California
Authors: Placzek Hilary , Cruz Stephanie , Chapdelaine Michelle , Carl Mary , Levin Sara , Hsu Clarissa 
Published: October 2021

AbstractBackgroundAddressing social risks in the clinical setting can increase patient confidence in the availability of community resources and may contribute to the development of a therapeutic alliance which has been correlated with treatment adherence and improved quality of life in mental health contexts. It is not well understood what barriers patients face when trying to connect to community resources that help address social risks. This paper aims to describe patient-reported barriers to accessing and using social needs-related resources to which they are referred by a program embedded in a safety net primary care clinic.MethodsThis is a qualitative assessment of patient-reported barriers to accessing and using social needs assistance programs. We conducted over 100 in-depth interviews with individuals in Northern California who participated in a navigation and referral program to help address their social needs and describe a unique framework for understanding how policies and systems intersect with an individual’s personal life circumstances.ResultsIndividuals described two distinct domains of barriers: 1) systems-level barriers that were linked to the inequitable distribution of and access to resources, and 2) personal-level barriers that focused on unique limitations experienced by each patient and impacted the way that they accessed services in their communities. While these barriers often overlapped or manifested in similar outcomes, this distinction was key because the systems barriers were not things that individuals could control or overcome through their own initiative or by increasing individual capacity.ConclusionsRespondents describe intersecting systemic and personal barriers that compound patients’ challenges to getting their social needs met; this includes both a picture of the inequitable distribution of and access to social services and a profile of the limitations created by individual life histories. These results speak to the need for structural changes to improve adequacy, availability, and accessibility of social needs resources. These findings highlight the need for advocacy to address systems barriers, especially the stigma that is faced by people who struggle with a variety of health and social issues, and investment in incentives to strengthen relationships between health care settings and social service agencies.
A case report of rhabdomyolysis and osteofascial compartment syndrome in a patient with hypothyroidism and diabetes
Authors: Ren Lijue , Wei Cuiying , Wei Feng , Ma Ruiting , Liu Yan , Zhang Yonghong , Wang Wei , Du Jing , Bai Lin , Xue Yexia , Cui Shaohua 
Published: October 2021

AbstractBackgroundHypothyroidism is frequent and has various forms of muscle involvement. We report the diagnosis and treatment of a case of rhabdomyolysis, bilateral osteofascial compartment syndrome (OCS) of the lower extremities, and peroneal nerve injury causing bilateral foot drop in a diabetic patient with hypothyroidism.Case presentationA 66-year-old man with diabetes for 22 years was admitted because of drowsiness, tiredness, facial swelling, and limb twitching for 2 months, and red and swollen lower limb skin for 3 days. Serum creatinine kinase (CK), CK-MB, myoglobin (Mb), blood glucose, and HbA1c were elevated. TSH, thyroid peroxidase antibodies, and antithyroglobulin antibodies were elevated. FT3 and FT4 were low. Urine was dark brown. He was diagnosed with hypothyroidism, rhabdomyolysis, and OCS. CK, CK-MB, and Mb returned to normal after treatment with thyroid hormone, insulin, albumin infusion, ceftriaxone, ulinastatin, and hemofiltration, and the redness and swelling of the lower limbs were relieved, but the patient developed dropping feet. The patient recovered well but had to undergo rehabilitation.ConclusionHypothyroidism may induce rhabdomyolysis, OCS, and other complications. This case reminds us of the importance of screening for hypothyroidism and strengthens the clinicians’ understanding of the disease.