bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lost in Translation: The Pitfalls of Ensembl Gene Annotations Between Human Genome Assemblies and Their Impact on Diagnostics
Authors: Abdallah Mohammed O.E , Koko Mahmoud , Ramesar Raj 
Published: December 2020

Abstract
Background:The GRCh37 human genome assembly is still widely used in genomics despite the fact an updated human genome assembly (GRCh38) has been available for many years. A particular issue with relevant ramifications for clinical genetics currently is the case of the GRCh37 Ensembl gene annotations which has been archived, and thus not updated, since 2013. These Ensembl GRCh37 gene annotations are just as ubiquitous as the former assembly and are the default gene models used and preferred by the majority of genomic projects internationally. In this study, we highlight the issue of genes with discrepant annotations, that have been recognized as protein coding in the new but not the old assembly. These genes are ignored by all genomic resources that still rely on the archived and outdated gene annotations. Moreover, the majority if not all of these discrepant genes (DGs) are automatically discarded and ignored by all variant prioritization tools that rely on the GRCh37 Ensembl gene annotations.Methods:We performed bioinformatics analysis identifying Ensembl genes with discrepant annotations between the two most recent human genome assemblies, hg37, hg38, respectively. Clinical and phenotype gene curations have been obtained and compared for this gene set. Furthermore, matching RefSeq transcripts have also been collated and analyzed. ٌResults:We found hundreds of genes (N=267) that were reclassified as “protein-coding” in the new hg38 assembly. Notably, 169 of these genes also had a discrepant HGNC gene symbol between the two assemblies.Most genes had RefSeq matches (N=199/267) including all the genes with defined phenotypes in Ensembl genes GRCh38 assembly (N=10). However, many protein-coding genes remain missing from the current known RefSeq gene models (N=68)Conclusion: We found many clinically relevant genes in this group of neglected genes and we anticipate that many more will be found relevant in the future. For these genes, the inaccurate label of “non-protein-coding” hinders the possibility of identifying any causal sequence variants that overlap them. In addition, Important additional annotations such as evolutionary constraint metrics are also not calculated for these genes for the same reason, further relegating them into oblivion.
High proportion of caesarean section at a rural hospital in south western Uganda:&nbsp;A cross sectional study
Authors: Nuwabaine Lilian , Mathius Amperiize , Nakalega Patience Annet 
Published: December 2020

Abstract
Background: Globally, overall prevalence of caesarean section (CS) is estimated at 18.6%, with 27% in high-income countries and 6% in low- and middle-income countries. There is an increase in trends of CS in Uganda from 8.5% in 2012 to 11% in 2016. There have been no studies done to account for the high rates of CS in a rural hospital in Uganda. This study determined the proportion and factors associated with CS delivery at a rural hospital in south western Uganda.Methods: This was a cross sectional study of 321 immediate postnatal women in a rural hospital in south western Uganda. A structured questionnaire and data abstract forms were used to collect information on proportion and factors associated with CS. Eligible participants were enrolled consecutively. Logistic regression analysis was done to identify the factors associated with CS taking into account potential confounders.Results: This study recruited 321 women with mean age of 25.8 ±6.086 years, mean parity 2.6 ±1.673 and mean antenatal care visits of 4.27 ±1.197. The proportion of CS in this study was 38.3% (123/321). Of these, 110 (89.4%) were emergencies and 27(10.6%) electives. Only 8.4% of the respondents were referrals. The commonest indications of CS were fetal distress (28.5%), history of previous CS (18.7%) and poor progress of labour (11.4%). No factors were significantly associated with CS in this study.Conclusion: There is a high proportion of CS in a rural hospital in Uganda and this is three times higher than the WHO recommended CS rates. Majority of CS are emergencies due to fetal distress and poor progress of labour. There is a need for additional studies exploring the reasons for the much higher than expected CS rates.
Ethnobotanical knowledge on non-conventional food and medicinal plants in Rio Cajari Extractivist Reserve, Amazon, Brazil
Authors: Filho Galdino Xavier de Paula , Ribeiro Adivair Freitas , Moraes Alcidete Flexa , Penha Willis Freitas , Borges Wardsson Lustrino , Santos Ricardo Henrique Silva 
Published: December 2020

Abstract
Background: Information on the knowledge, management and ways of using food and medicinal plants by traditional populations, family farmers and Brazilian native population in the Amazon is essential to guarantee the sovereignty of these groups. The objective of this study was to evaluate the diversity, knowledge and ways of using non-conventional food and medicinal plants in traditional communities in a conservation unit in the Brazilian Amazon.Methods: This study was conducted using semi-structured interviews applied to local respondents. Fifty-six residents were interviewed in 26 communities. The Indices of Use Value (UVI) and relative frequency of species citation (Fr) were evaluated; also, their diversity and equitability using the Shannon- Wiener (H’) Pielou (J’) indices, respectively. The species were listed according to their family, scientific name, popular names, categories of use, propagation environment, growth habit, medicinal indications, domestication status, production cycle and herbarium registration.Results: A total of 269 species of both non-conventional food and medicinal plants were identified, distributed in 83 botanical families, 198 genera, in addition to 13 unidentified species. The Arecaceae and Lamiaceae families had the highest species richness (11 and 7, respectively). Eryngium foetidum L. (Apiaceae) and Ipomoea potatoes L. (Convolvulaceae) presented the highest relative citation frequencies (19.7 and 19.3, respectively) and the highest index of use value of the species (0.94 and 0.92, respectively). The Shannon-Wiener (H’) and Pielou (J’) diversity indices were considered high (5.02 and 0.9, respectively) when compared to other ethnobotanical works carried out in Brazil and in the Amazon.Conclusions: A wide relationship of use was observed between the species under study and the population of this conservation area. In the environment in which these families are found, of geographical isolation and distance from urban centers, these species become, in many circumstances, the only food and medicinal resources, therefore, being fundamental to the sovereignty of these families.
Impact of Urgent and Emergency Care Vanguards on Delayed Transfers of Care in England
Authors: Malisauskaite Gintare , Jones Karen , Allan Stephen , Roland Daniel , Birks Yvonne , Baxter Kate , Gridley Kate 
Published: December 2020

Abstract
Objectives: To assess the relationship between Urgent and Emergency Care (UEC) Vanguards, which include as an aim the integration of healthcare and social care sectors, and Delayed Transfers of Care (DTOC) at Local Authority level in England. Methods: Difference-in-difference pooled cross section, fixed and random effects panel estimations were used to compare DTOC between UEC partner site Local Authorities with non-UEC Local Authorities employing quarterly data on days of DTOC from Local Authorities in England for the period 2010 to 2017. Robustness checks included employing a range of sample and variable specifications and synthetic control estimations.Results: A statistically significant negative relationship was found between UEC Vanguards and DTOC rates that is robust to various specification checks with no indication of UEC participant sites having lower DTOC rates prior to the start of the initiative. Conclusions:UEC Vanguards appear to be associated with up to 40.5% lower DTOC rates at 1% significance level compared with other English Local Authorities. The empirical evidence indicates a statistically significant impact; however, more research is required to explain the reasons for this relationship.
Study of dynamic vibration characteristics and suppression of CNC machine tool during operation
Authors: Qiu Chao , Chen Xingzhou , Hui Yanbo , Siddiquee Tahir Abdul Rahman 
Published: December 2020

The rapid development of aerospace, automobile, national defense and other manufacturing industries has continuously improved the performance requirements of high speed and high positioning accuracy of the CNC machine tool feed system. As the thermal deformation error increases, the system structural rigidity decreases, the vibration increases, and accuracy of machine tool reduces. Existing research mainly focuses on the properties of mechanical and single thermal feed system, and less considers the dynamic performance under the action of thermal-mechanical coupling. For the improvement of feed system performance, it is very beneficiary. This paper takes the high-speed tool of CNC feed system as objective, combined with the actual working conditions to analyze the thermal characteristics, dynamic characteristics and vibration characteristics of the system under the effect of thermal-mechanical coupling. The thermal resistance and convective heat transfer of the key joint surface, the application of moving thermal loads, and the establishment of a simulation model to complete the steady-state temperature field, transient temperature field and thermal-structure coupling analysis. The results show that the maximum temperature rise of the feed system is 21.08 °C, The maximum thermal deformation is 17.264 um. The study found that the parameters such as flow rate and airflow temperature have a significant impact on the cooling effect, so the cooling device was further optimized. This paper proposes a control method for cutting chatter of CNC machine tools based on coupling of characteristics of thermal and mechanical. The thermal characteristic of the feed system and the thermal-mechanical coupling vibration characteristic test provides the maximum temperature error of 3.2 %, verifying the correctness of the theoretical method and analysis model. The highest temperature obtained by the test is 39.7 °C, indicating that the high-speed feed system has a large thermal effect. The relative error of the vibration amplitude of the test and simulation is 12.5 %, which verifies coupling in terms of thermal-mechanical. The accuracy of the vibration analysis method; the experiment depicts that the vibration amplitude increases by 19.7 % under the coupling effect of thermal and mechanical, indicating the effectiveness of dynamic characteristics of the high-speed feed system considering the thermal-mechanical coupling effect.
Development and Characteristics of Novel PLGA-chitosan as a New Nanocarrier for Pentavalent Vaccine Delivery
Authors: Alikhani Zahra , Kazemi-Pour Nadia , Shafieeardestani Mehdi , Noofeli Mojtaba 
Published: December 2020

Background:
Lately, the employment of nano-carriers has been known as an optimistic means of drug and
vaccine delivery.

Objective:
Nano vaccines are a novel tier of vaccines that can develop humoral and cellular immune
responses and can be introduced as a practical and secure nano vaccine candidate for the prevention
of diseases. The purpose of this study was to accomplish and use biodegradable nano-carriers for the
synthesis of pentavalent vaccine and immunogenicity evaluation in the animal models. The PLGA
nanoparticle was prepared and modified with chitosan nanoparticles. Nano-carrier PLGA-chitosan
was loaded by the DTP-HepB-Hib antigens and confirmed by DLS, SEM, TEM and FT-IR, then
in vitro loading and release were evaluated. Toxicity was assessed by the MTT method in the
Hec293 cells. Antigenicity evaluation and histopathological study were conducted by injection of
new nano pentavalent vaccines in the BALB/c mice and the immune response was measured in the
serum samples through an indirect ELISA method.

Results:
Conclusions drawn from the current study exhibited the plausible ability of nano-carrier to
deliver the vaccine. A notable increase was shown in total IgG and IgM antibodies examined in
mice vaccinated with new nano vaccines. The histopathological study in the treated mice showed no
toxicity in the vital organs of mice.

Conclusion:
The engineered vaccine delivery system showed the ability to induce robust immune responses and also the
suitability features of the PLGA-chitosan as a promising carrier to improve vaccine delivery.
Synthesis, Anti-Bacterial and Anti-Oxidant Activity of Azo-Oxazolone and Their Ring Opening Azo-Benzamide Derivatives
Authors: Ayoob Mzgin M. , Hussein Awaz J. , Samad Mohammed K. , Dege Necmi , Hawaiz Farouq E. , Mohamed Shaaban K. , Hussain Faiq H.S. 
Published: December 2020

Aims:
This article describes the controlled synthesis and characterization of azo oxazolone scaffold compounds
containing multifunctional groups such as carbonyl group, imine and carbon-carbon double bond. The
reaction of the azo-oxazolone with aromatic amines led to the ring-opening of the azo-oxazolone into the corresponding
azo-benzamide derivatives in a short time (average 10 min), resulting in high yield (>90%). All newly
synthesized compounds were characterized by the common spectral analysis such as UV, IR, 1H-NMR, 13CNMR,
Elemental analysis and MS spectrometry.

Objective:
The aim of the study was to synthesize new bioactive azo-benzamides by using azo-oxazolone as a
synthon utilizing its ring-opening function.

Materials and Methods:
Azo-benzamide derivatives were prepared in very good yield via ring-opening reaction
of azo-oxazolone with aromatic amines in the presence of acetic acid under reflux for few minutes.

Conclusion:
The new azo-oxazolone 4 and azo-benzamide compounds 5a, 5c, 5f, 5h, 5j were screened against
Escherichia coli as G(-ve) and Staphylococcus aureus as G(+ve) using ciprofloxacin as a standard. All compounds
showed high inhibition potency against E-Coli but low inhibition for S-aureus. Compounds 4, 5c, and 5J
showed more reactivity against E-coli.

Others:
Others: Also, the compounds were tested for their anti-oxidant activity by both DPPH and FRAP methods. The
results showed that some compounds possessed moderate anti-oxidant activity in comparison to ascorbic acid as
control, typically the compounds bearing OCH3 and OCH2CH3 groups.
Evaluation of Salivary Helicobacter pylori, Calcium, Urea, pH and Flow Rate in Hemodialysis Patients
Authors: Teimoori Farshad , Hajilooei Mehrdad , Abdolsamadi Hamidreza , Eslami Khadijeh , Moghimbeigi Abbas , Ahmadi- Motamayel Fatemeh 
Published: December 2020

Background:
Helicobacter pylori infection identified as a major cause of stomach ulcers, chronic inflammation
and gastric cancer in hemodialysis patients. Dialysis also leads to changes in the composition and flow of saliva.

Objective:
The aim of this study was to investigate the salivary Helicobacter pylori infection, Calcium, Urea, pH and flow
rate in hemodialysis patients in comparison to the healthy control group.

Method:
In this study 48 hemodialysis patients and 48 healthy subjects were compared. The prevalence of Helicobacter pylori infection was determined by PCR method. Calcium, Urea, pH, salivary flow and gastrointestinal complications in both
groups were measured and compared.

Results:
Prevalence of Helicobacter pylori was 12.48 (25.0%) in the study group and 2.48 (4.2%) in the controls. (P=0.000).
Urea, calcium and pH were significantly higher in the patient group .The mean salivary flow rate decreased significantly in
the patient group. 58.3% of patients group had gastrointestinal complications.

Conclusion:
Oral cavity as an important external source of Helicobacter pylori may play an important role in gastrointestinal problems of hemodialysis patients. Helicobacter pylori, Urea, calcium and pH were significantly higher in the patient
group .Chronic renal failure can increase pH, urea and calcium in saliva and decrease salivary flow rate.
An Ensemble of Bacterial Foraging, Genetic, Ant Colony and Particle
Swarm Approach EB-GAP: A Load Balancing Approach in Cloud
Computing
Authors: Dewangan Bhupesh Kumar , Choudhury Tanupriya , Jain Anurag , Shukla Ram Narayan 
Published: December 2020

Background:
In the cloud environment, satisfaction of service level agreement (SLA) is the prime objective. It
can be achieved by providing services in minimum time in an efficient manner at the lowest cost by efficiently utilizing
the resources. This will create a win-win situation for both consumer and service provider. Through literature analysis, it
has been found that the procedure of resource optimization is quite costly and time-consuming.

Objective:
The research aim is to design and develop an efficient load-balancing technique for the satisfaction of service
level agreement and the utilization of resources in an efficient manner.

Methods:
To achieve this, authors have proposed a new load-balancing algorithm named eB-GAP by picking the best
features from Bacterial Foraging, Genetic, Particle-Swarm, and Ant-Colony algorithm. Based on the availability of
resources and load on a virtual machine, a fitness value is assigned to all virtual machines.

Results:
A newly arrived task is mapped with the fittest virtual machine. Whenever a new task is mapped or left the
system, the fitness value of the virtual machine is updated. In this manner, the system achieves the satisfaction of service
level agreement, the balance of the load, and efficient utilization of resources. To test the proposed approach, the authors
have used the real-time cloud environment of amazon web service. In this, waiting time, completion time, execution time,
throughput, and cost have been computed in a real-time environment.
Predictors and Consequences of Veterans Affairs Mental Health Provider Burnout: Protocol for a Mixed Methods Study
Authors: Zivin Kara , Kononowech Jennifer , Boden Matthew , Abraham Kristen , Harrod Molly , Sripada Rebecca K , Kales Helen C , Garcia Hector A , Pfeiffer Paul 
Published: December 2020

Background
In the Veterans Health Administration (VHA), mental health providers (MHPs) report the second highest level of burnout after primary care physicians. Burnout is defined as increased emotional exhaustion and depersonalization and decreased sense of personal accomplishment at work.

Objective
This study aims to characterize variation in MHP burnout by VHA facility over time, identifying workplace characteristics and practices of high-performing facilities.

Methods
Using both qualitative and quantitative methods, we will evaluate factors that influence MHP burnout and their effects on patient outcomes. We will compile annual survey data on workplace conditions and annual staffing as well as productivity data to assess same and subsequent year provider and patient outcomes reflecting provider and patient experiences. We will conduct interviews with mental health leadership at the facility level and with frontline MHPs sampled based on our quantitative findings. We will present our findings to an expert panel of operational partners, Veterans Affairs clinicians, administrators, policy leaders, and experts in burnout. We will reengage with facilities that participated in the earlier qualitative interviews and will hold focus groups that share results based on our quantitative and qualitative work combined with input from our expert panel. We will broadly disseminate these findings to support the development of actionable policies and approaches to addressing MHP burnout.

Results
This study will assist in developing and testing interventions to improve MHP burnout and employee engagement. Our work will contribute to improvements within VHA and will generate insights for health care delivery, informing efforts to address burnout.

Conclusions
This is the first comprehensive, longitudinal, national, mixed methods study that incorporates different types of MHPs. It will engage MHP leadership and frontline providers in understanding facilitators and barriers to effectively address burnout.

International Registered Report Identifier (IRRID)
PRR1-10.2196/18345
SOSIALISASI DIVERSIFIKASI PRODUK PANGAN FUNGSIONAL BERBASIS SORGUM DI DESA CIMANGGU KECAMATAN PAMEUNGPEUK KABUPATEN BANJARAN
Authors: Wulandari Endah , Sukarminah Een , Lembong Elazmanawati 
Published: December 2020

Biji sorgum memiliki kandungan gizi yang baik, seperti karbohidrat, protein, lemak, mineral, dan vitamin, serta tidak mengandung gluten seperti yang terdapat di dalam gandum, sehingga aman untuk penderita penyakit intoleran terhadap gluten seperti autisme, penyakit seliak, dan lain sebagainya. Tujuan dari program ini adalah sosialisasi diversifikasi produk pangan berbasis sorgum menjadi pangan fungsional, membangun kesadaran untuk memulai berwirausaha dan mengembangkan industri rumah tangga berdasarkan potensi pangan lokal yang dimiliki demi perbaikan kesejahteraan keluarga dan masyarakat sekitar dan melakukan penyuluhan/penyadaran tentang cara pengolahan pangan yang baik dan benar. Hasil dari proses PPM adalah respon warga masyarakat dan aparat kecamatan Pamengpeuk Kabupaten Bandung baik dan positif terhadap kegatan PPM yang akan dilaksanakan selama bulan April sampai dengan Desember 2018 Respon aparat desa sayang dan ibu PKK baik dan mendukung kegiatan dengan batuan perijinan penggunaan fasilitas desa.
Fenomena Kasus Bunuh Diri akibat Ijime pada Anak SMP di Jepang
Authors: Nasution Yenny Aristia 
Published: December 2020

Ijime adalah sebuah fenomena yang terbentuk akibat ditemukannya fenomena seseorang yang mem-bully dan seseorang yang menjadi korban dari ijime tersebut. Di Jepang, ijime menjadi salah satu masalah serius dalam dunia pendidikan sejak tahun 1970-an dan alasan utamanya dilatarbelakangi oleh kenaikan angka persentase bunuh diri anak usia sekolah. Hal ini dapat dilihat pada persentase jumlah kasus ijime yang terjadi pada setiap tahunnya dan juga berdasarkan dari bentuk ijime sekolah yang sering dilaporkan ke media massa. Penelitian ini bertujuan untuk mengetahui bentuk bunuh diri yang diakibatkan oleh ijime pada anak SMP di Jepang, memaparkan alasan kasus bunuh diri akibat ijime yang banyak terjadi pada anak SMP di Jepang, dan memaparkan penyebab perilaku ijime yang mengakibatkan bunuh diri pada anak SMP di Jepang. Peneliti menggunakan teori strukturisasi yang dikemukakan oleh Anthony Giddens dalam menganalisis tindakan anak yang di-bully atau mendapat perlakuan ijime yang menyebabkan keinginan untuk melakukan tindakan bunuh diri. Penelitian ini menggunakan metode penelitian kualitatif dengan menggunakan metode kajian pustaka. Dari hasil penelitian ini ditemukan bahwa ijime lebih banyak terjadi pada anak-anak di kalangan SMP, karena masa SMP adalah suatu masa anak-anak mulai menginjak usia remaja dan para korban ijime lebih banyak melakukan tindakan bunuh diri dengan cara menggantung diri dan terjun dari atas atap apartemen. Jenis bunuh diri yang banyak terjadi pada kasus ini adalah bunuh diri anomik dan jenis bunuh diri yang paling sedikit terjadi pada kasus ini adalah bunuh diri egoistik dan bunuh diri anomik, dan para korbannya banyak meninggalkan surat (suicide note) sebelum melakukan bunuh diri.
Kata kunci: anak SMP; bunuh diri; ijime; suicide note