bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spectrum of association in HLA region with rheumatoid arthritis in a diverse Asian population: evidence from the MyEIRA case-control study
Authors: Tan Lay Kim , Too Chun Lai , Diaz-Gallo Lina Marcela , Wahinuddin Sulaiman , Lau Ing Soo , Heselynn Hussein , Nor-Shuhaila Shahril , Gun Suk Chyn , Eashwary Mageswaran , Mohd-Shahrir Mohamed Said , Ainon Mohd Mokhtar , Azmillah Rosman , Muhaini Othman , Shahnaz Murad , Alfredsson Lars , Klareskog Lars , Padyukov Leonid 
Published: January 2021

Abstract
Background
Fine-mapping of human leukocyte antigen (HLA) region for rheumatoid arthritis (RA) risk factors has identified several HLA alleles and its corresponding amino acid residues as independent signals (i.e., HLA-A, HLA-B, HLA-DPB1, and HLA-DQA1 genes), in addition to the well-established genetic factor in HLA-DRB1 gene. However, this was mainly performed in the Caucasian and East Asian populations, and data from different Asian regions is less represented. We aimed to evaluate whether there are independent RA risk variants in both anti-citrullinated protein antibody (ACPA)-positive and ACPA-negative RA patients from the multi-ethnic Malaysian population, using the fine-mapping of HLA region strategy.

Methods
We imputed the classical HLA alleles, amino acids, and haplotypes using the Immunochip genotyping data of 1260 RA cases (i.e., 530 Malays, 259 Chinese, 412 Indians, and 59 mixed ethnicities) and 1571 controls (i.e., 981 Malays, 205 Chinese, 297 Indians, and 87 mixed ethnicities) from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA) population-based case-control study. Stepwise logistic regression was performed to identify the independent genetic risk factors for RA within the HLA region.

Results
We confirmed that the HLA-DRB1 amino acid at position 11 with valine residue conferred the strongest risk effect for ACPA-positive RA (OR = 4.26, 95% CI = 3.30–5.49, PGWAS = 7.22 × 10−29) in the Malays. Our study also revealed that HLA-DRB1 amino acid at position 96 with histidine residue was negatively associated with the risk of developing ACPA-positive RA in the Indians (OR = 0.48, 95% CI = 0.37–0.62, PGWAS = 2.58 × 10−08). Interestingly, we observed that HLA-DQB1*03:02 allele was inversely related to the risk of developing ACPA-positive RA in the Malays (OR = 0.17, 95% CI = 0.09–0.30, PGWAS = 1.60 × 10−09). No association was observed between the HLA variants and risk of developing ACPA-negative RA in any of the three major ethnic groups in Malaysia.

Conclusions
Our results demonstrate that the RA-associated genetic factors in the multi-ethnic Malaysian population are similar to those in the Caucasian population, despite significant differences in the genetic architecture of HLA region across populations. A novel and distinct independent association between the HLA-DQB1*03:02 allele and ACPA-positive RA was observed in the Malays. In common with the Caucasian population, there is little risk from HLA region for ACPA-negative RA.
Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing
Authors: Papoutsis Andreas , Borody Thomas , Dolai Siba , Daniels Jordan , Steinberg Skylar , Barrows Brad , Hazan Sabine 
Published: January 2021

Abstract
Background
SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients.

Results
Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS.

Conclusion
These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.
Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).
The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air
Authors: Premkrishnan Balakrishnan N. V. , Heinle Cassie E. , Uchida Akira , Purbojati Rikky W. , Kushwaha Kavita K. , Putra Alexander , Santhi Puramadathil Sasi , Khoo Benjamin W. Y. , Wong Anthony , Vettath Vineeth Kodengil , Drautz-Moses Daniela I. , Junqueira Ana Carolina M. , Schuster Stephan C. 
Published: January 2021

Abstract
Background
Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and biofilms contribute to their pathogenicity, classified in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap-free, whole-genome sequences of two B. cereus strains isolated from air samples and analyse their emetic and diarrheal potential.

Results
Genome assemblies of the B. cereus strains consist of one chromosome and seven plasmids each. The genome size of strain SGAir0260 is 6.30-Mb with 6590 predicted coding sequences (CDS) and strain SGAir0263 is 6.47-Mb with 6811 predicted CDS. Macrosynteny analysis showed 99% collinearity between the strains isolated from air and 90.2% with the reference genome. Comparative genomics with 57 complete B. cereus genomes suggests these strains from air are closely associated with strains isolated from foodborne illnesses outbreaks. Due to virulence potential of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confirmed resistance to ampicillin and fosfomycin, with susceptibility to ciprofloxacin, tetracycline and vancomycin in both strains.

Conclusion
Phylogenetic analysis combined with detection of haemolytic (hblA, hblC, and hblD) and non-haemolytic (nheA, nheB, and nheC) enterotoxin genes in both air-isolated strains point to the diarrheic potential of the air isolates, though not emetic. Characterization of these airborne strains and investigation of their potential disease-causing genes could facilitate identification of environmental sources of contamination leading to foodborne illnesses and nosocomial infections transported by air.
Bacterial contamination of neonatal intensive care units: How safe are the neonates?
Authors: Bhatta Dharm Raj , Hosuru Subramanya Supram , Hamal Deependra , Shrestha Rajani , Gauchan Eva , Basnet Sahisnuta , Nayak Niranjan , Gokhale Shishir 
Published: January 2021

Abstract
Background
Intensive care units (ICU) are essential healthcare facility for life threatening conditions. Bacterial contamination of objects/instruments in ICU is an important source of nosocomial infections. This study is aimed to determine the level of bacterial contamination of instruments/objects which are commonly touched by healthcare workers and frequently come in contact with the neonates.

Methods
This hospital based prospective study was conducted in neonatal intensive care unit (NICU) of Manipal Teaching Hospital, Pokhara, Nepal. A total of 146 samples collected from surfaces of incubators, radiant warmers, suction tips, ventilators, stethoscopes, door handles, weighing machines, mothers’ beds, phototherapy beds, laryngoscope, telephone sets, blood pressure machine, etc. formed the material of the study. Isolation, identification and antibiotic susceptibility of the bacterial isolates was performed by standard techniques. Blood culture isolates from NICU patients during the study period were compared with the environmental isolates.

Results
Out of 146 samples, bacterial growth was observed in 109. A total of 119 bacterial isolates were retrieved from 109 samples. Three common potential pathogens isolated were Escherichia coli (n = 27), Klebsiella species (n = 21) and Staphylococcus aureus (n = 18). Majority of E. coli and Klebsiella isolates were from incubators, suction tips and mothers’ beds. Majority of S. aureus isolates were cultured from radiant warmers. Among S. aureus isolates, 33.3% (6/18) were methicillin resistant. Majority of the bacterial isolates were susceptible to gentamicin and amikacin. Common potential pathogens isolated from blood culture of NICU patients were S. aureus and Klebsiella species.

Conclusion
High degree of bacterial contamination of objects/instruments in NICU was recorded. Isolation of potential pathogens like E. coli, Klebsiella species and S. aureus is a major threat of nosocomial infections. Blood culture data of NICU reflects possibility of nosocomial infections from contaminated sites. Gentamicin and amikacin may be used for empirical therapy in suspected cases of nosocomial infections in NICU.
LncRNA APCDD1L-AS1 induces icotinib resistance by inhibition of EGFR autophagic degradation via the miR-1322/miR-1972/miR-324-3p-SIRT5 axis in lung adenocarcinoma
Authors: Wu Jie , Zheng Chunlei , Wang Yizhe , Yang Zichang , Li Ce , Fang Wanxia , Jin Yue , Hou Kezuo , Cheng Yang , Qi Jianfei , Qu Xiujuan , Liu Yunpeng , Che Xiaofang , Hu Xuejun 
Published: January 2021

Abstract
Background
Epidermal growth factor receptor-tyrosinase kinase inhibitor (EGFR-TKI) resistance is the major obstacle in the treatment of lung adenocarcinoma (LUAD) patients harboring EGFR-sensitive mutations. However, the long non-coding RNAs (lncRNAs) related to EGFR-TKIs resistance and their functional mechanisms are still largely unknown. This study aimed to investigate the role and regulatory mechanism of lncRNA APCDD1L-AS1 in icotinib resistance of lung cancer.

Methods
Molecular approaches including qRT-PCR, MTT assay, colony formation, RNA interference and cell transfection, RNA immunoprecipitation (RIP), dual luciferase reporter assay, RNA fluorescence in situ hybridization, TUNEL assay, flow cytometry, immunoblotting, xenograft model and transcriptome sequencing were used to investigate the mechanism of APCDD1L-AS1 in icotinib resistance.

Results
A novel lncRNA, APCDD1L-AS1 was identified as the most significantly upregulated lncRNA in icotinib-resistant LUAD cells by the transcriptome sequencing and differential lncRNA expression analysis. We found that APCDD1L-AS1 not only promoted icotinib resistance, but also upregulated the protein expression level of EGFR. Mechanistically, APCDD1L-AS1 promoted icotinib resistance and EGFR upregulation by sponging with miR-1322/miR-1972/miR-324-3p to remove the transcription inhibition of SIRT5. Furthermore, SIRT5 elevated EGFR expression and activation by inhibiting the autophagic degradation of EGFR, finally promoting icotinib resistance. Consistently, the autophagy initiator rapamycin could decrease EGFR levels and increase the sensitivity of icotinib-resistant LUAD cells to icotinib.

Conclusion
APCDD1L-AS1 could promote icotinib resistance by inhibiting autophagic degradation of EGFR via the miR-1322/miR-1972/miR-324-3p-SIRT5 axis. The combination of autophagy initiator and EGFR-TKIs might serve as a potential new strategy for overcoming EGFR-TKIs resistance in LUAD patients.
Understanding social media beyond text: a reliable practice on Twitter
Authors: Hou Qixuan , Han Meng , Qu Feiyang , He Jing Selena 
Published: January 2021

AbstractSocial media provides high-volume and real-time data, which has been broadly used in diverse applications in sales, marketing, disaster management, health surveillance, etc. However, distinguishing between noises and reliable information can be challenging, since social media, a user-generated content system, has a great number of users who update massive information every second. The rich information is not only included in the short textual content but also embedded in the images and videos. In this paper, we introduce an effective and efficient framework for event detection with social media data. The framework integrates both textual and imagery content in the hope to fully utilize the information. The approach has been demonstrated to be more accurate than the text-only approach by removing 58 (66.7%) false-positive events. The precision of event detection is improved by 6.5%. Besides, based on our analysis, we also look into the content of these images to further explore the space of social media studies. Finally, the closely related text and image from social media offer us a valuable text-image mapping, which can enable knowledge transfer between two media types.
The effect of alcohol strength on alcohol consumption: findings from a randomised controlled cross-over pilot trial
Authors: Perman-Howe Parvati R. , Davies Emma L. , Foxcroft David R. 
Published: January 2021

Abstract
Background
Reducing the alcohol content of drinks has the potential to reduce alcohol consumption. The aims of this study are to (1) test the feasibility of a randomised controlled trial (RCT) to assess the effect of alcohol strength on alcohol consumption within licensed premises in the United Kingdom (UK), and to (2) provide data to estimate key parameters for a RCT.

Methods
This study is a double-blind randomised controlled cross-over pilot trial based within four licensed premises in the UK. Participants (n = 36) purchased and consumed ad libitum a 3.5% lager and a 4.8% lager during two separate study sessions. Descriptive statistics reported the efficacy and efficiency of the study processes, and the rates of licensed premises recruitment, and participant recruitment and attrition. Mean and the 95% confidence interval (CI) compared alcohol consumption between conditions. The mean, standard deviation (SD) and CI of UK units of alcohol consumed were used to calculate a sample size for a RCT. Responses to participant questionnaires and duration of participation in study sessions between conditions were analysed.

Results
Components of the study protocol were effective and efficient. The venue recruitment rate was less than anticipated. The participant recruitment rate was greater than anticipated. The rate of attrition was 23% and varied by less than 1% according to the arm of the trial. There was a reduction of alcohol consumed under the intervention conditions. Estimated mean difference, and 95% CI (UK units): − 3.76 (− 5.01 to − 2.52). The sample size required for a RCT is 53. Participants did not find one lager more pleasant in taste: (on a scale of one to 10) − 0.95 (− 2.11 to 0.21). Participants found the reduced-strength lager less enjoyable: (on a scale of one to 10) − 1.44 (− 2.64 to − 0.24) and they perceived themselves to be less intoxicated after consuming it: (on a scale of one to 10) − 1.00 (− 1.61 to − 0.40).

Conclusion
A RCT is feasible with minor alterations to the study protocol and scoping work to establish different brands of alcohol that are more alike and more enjoyable than the products used in the pilot trial.

Trial registration
Registered in the American Economic Association (AEA) Randomised Controlled Trial (RCT) Registry as of 16 June 2017. Unique identifying number: AEARCTR-0002266.
City residents, scientists and policy-makers: power in co-producing knowledge
Authors: Buyana Kareem , Walubwa Jacqueline , Mukwaya Paul , Lwasa Shuaib , Owuor Samuel 
Published: January 2021

AbstractThe need to merge scientific with societal knowledge in addressing global sustainability challenges has deepened research on a methodology known as co-producing knowledge. It differs from participatory approaches by holding potential for solution-oriented research through sustained relationships with actors across disciplines and sectors. Although there is growing recognition that power shapes interactions in co-producing knowledge, few studies have empirically grounded articulations of power in the context of urban sustainability. This paper draws on case study projects in Africa to discern the forms of power that are navigated by actors when co-producing locally grounded knowledge and solutions for urban sustainability. The projects include: localizing norms on sustainable energy in Kampala city Uganda; confronting coastal vulnerability in Durban South Africa; and upgrading informal settlements in Stellenbosch South Africa. The forms of power across the projects are: expert power by academics; statutory power for policy-makers; and the power of locally-embedded knowledge by city residents. Navigating these forms of power is possible, if boundary objects are used in dialogues on scalable solutions to sustainability challenges. The boundary objects in the case studies are: briquettes from organic waste as alternative cooking energy for households in Kampala; a locally-appropriate costal vulnerability index for visioning sustainable climate action in Durban; and an improved Shack dwelling for improving living conditions in Stellenbosch. These boundary objects interrupted the reproduction of unequal power relations, while demonstrating how hierarchies in co-producing knowledge can be flattened.
Spinal Cord Anatomy and Localization
Authors: Hardy Todd A. 
Published: January 2021

ABSTRACT

PURPOSE OF REVIEW
This article focuses on clinically relevant teaching points in spinal anatomy and localizing the lesion in myelopathy.

RECENT FINDINGS
The principles underlying spinal cord lesion localization are well established, but improvements in MRI and the discovery of pathologic antibodies associated with causes of transverse myelitis distinct from multiple sclerosis, such as aquaporin-4 IgG and myelin oligodendrocyte glycoprotein IgG, have assisted in diagnosis.

SUMMARY
The spinal cord has a highly organized neuroanatomy of ascending and descending tracts that convey sensory, motor, and autonomic information. Using integration of clues from the patient’s history and neurologic examination, the effective clinician can distinguish spinal cord from peripheral nerve or brain pathology, often determine the level and parts of the spinal cord affected by a lesion, and focus on a likely diagnosis. The advent of MRI of the spine has revolutionized investigation of spinal cord disorders, but an important place for strong clinical acumen still exists in assessing the patient with a myelopathy.
Myelitis and Other Autoimmune Myelopathies
Authors: Lopez Chiriboga Sebastian , Flanagan Eoin P. 
Published: January 2021

ABSTRACT

PURPOSE OF REVIEW
This article provides an update on the clinical diagnosis and management of immune-mediated myelopathies, including the relevance of imaging, ancillary testing with an emphasis on autoantibody biomarkers, recognition of myelitis mimics, and therapeutic approach.

RECENT FINDINGS
The imaging characterization of immune-mediated myelopathies and the discovery of neural autoantibodies have been crucial in improving our ability to accurately diagnose myelitis. The identification of autoantibodies directed against specific central nervous system targets has led to major improvements in our understanding of the mechanisms underlying inflammation in myelitis. It has also allowed distinction of these myelopathy etiologies from noninflammatory etiologies of myelopathy and from multiple sclerosis and provided insight into their risk of recurrence, treatment response, and long-term clinical outcomes. Prompt recognition and appropriate testing in the setting of acute and subacute myelopathies is critical as timely administration of immunotherapy can help improve symptoms and prevent permanent neurologic disability. A patient should not be classified as having “idiopathic transverse myelitis” without a comprehensive evaluation for a more specific etiology. Achieving the correct diagnosis and learning to recognize noninflammatory myelitis mimics is crucial as they have therapeutic and prognostic implications.

SUMMARY
Identifying the clinical and radiographic features of immune-mediated myelitis and recognizing mimics and pitfalls will help clinicians treat confirmed autoimmune myelitis appropriately.
Hereditary Myelopathies
Authors: Fink John K. 
Published: January 2021

ABSTRACT

PURPOSE OF REVIEW
This article guides clinicians in the clinical recognition and differential diagnosis of hereditary myelopathies.

RECENT FINDINGS
Rather than a disease, a disease process, or relating to specific cellular vulnerability, the term hereditary myelopathy refers to diverse inherited disorders in which major aspects of the clinical syndrome reflect disturbance of elements within the spinal cord (specifically, the dorsal columns and dorsal root ganglia, corticospinal tracts, and anterior horn cells). It is important to note that the clinical features of almost all hereditary myelopathies reflect not only disturbance of elements within the spinal cord but also disturbance of extraspinal structures (particularly, but not limited to, peripheral nerves and the cerebellum) and that these extraspinal clinical features can be very helpful in recognizing specific myelopathy syndromes. The value of classifying disorders as inherited myelopathies lies primarily in facilitating their clinical recognition and differential diagnosis. It is useful to recognize that many hereditary myelopathies conform to one of four clinical paradigms: (1) spinocerebellar ataxia, (2) motor neuron disorder, (3) leukodystrophy, or (4) distal motor-sensory axonopathy predominantly affecting the central nervous system. Although they are myelopathies, spinal dysraphisms such as spina bifida and myelomeningocele are not included in this context because they are not usually due to single-gene mutation and have low hereditability.

SUMMARY
This article illustrates clinical paradigms of hereditary myelopathy with clinical examples emphasizing the spectrum, clinical recognition, and differential diagnosis of hereditary myelopathies.
Shame, guilt, time perspective, time of imprisonment and PTSD symptoms in sentenced motor vehicle accidents perpetrators – a preliminary report
Authors: Merecz-Kot Dorota , Wężyk Agata , Waszkowska Małgorzata , Andysz Aleksandra 
Published: January 2021

Cel pracyBadanie koncentrowało się na związku pomiędzy objawami PTSD, poczuciem winy związanym z traumą, perspektywą czasową, oraz skłonnością do poczucia winy/wstydu u osadzonych sprawców wypadków samochodowych. Przeanalizowano także związki pomiędzy długością kary, objawami PTSD i poczuciem winy związanym z traumą.MetodaPróba badawcza składała się z 37 osadzonych sprawców wypadków drogowych. Poproszono ich o wypełnienie zestawu kwestionariuszy: Inwentarza Perspektywy Czasowej Zimbardo, Inwentarza Poczucia Winy i Wstydu, i Inwentarza Winy Związanej z Traumą.WynikiWyniki wykazały, że 50% sprawców spełniało kryteria DSM-5 dotyczące PTSD. Skłonność do poczucia winy i wstydu pozytywnie korelowała z poczuciem winy związanym z traumą. Podatność na poczucie wstydu jako konsekwencja negatywnej samooceny wiązała się także z większym poczuciem wstydu związanym z traumą. Nie wykazano korelacji pomiędzy skłonnością do poczucia winy/wstydu lub poczuciem winy związanym z traumą a objawami PTSD. Perspektywa czasowa wiązała się z objawami PTSD - im silniejsza u badanych była tendencja do koncentrowania się na teraźniejszości/przeszłości, tym większe objawy PTSD. Koncentracja na teraźniejszości pozytywnie korelowała z poczuciem winy związanym z traumą.WnioskiW badanej populacji co drugi sprawca wypadku dotknięty był PTSD, które wiązało się z przeszłą i teraźniejszą perspektywą czasową. Negatywna ocena siebie i swojego zachowania intensyfikowała poczucie winy związane z traumą i zmniejszała poszukiwanie usprawiedliwienia dla własnych czynów w okolicznościach zewnętrznych. Czas spędzony w więzieniu nie miał wpływu na postawę moralną i nie wpływał na moralną ocenę własnego zachowania, które spowodowało krzywdę innych osób. Wiązał się jednak z przeżywaniem stresu i skupieniem na własnym cierpieniu.