bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding and extending ancient simple sequence repeat-derived regions in the human genome
Authors: Shortt Jonathan A. , Ruggiero Robert P. , Cox Corey , Wacholder Aaron C. , Pollock David D.
Published: February 2020

Background

Previously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, and some of the unidentified regions are likely to be ancient SSR-derived regions not identified by current methods. The identification of these regions is complicated because SSRs appear to evolve through complex cycles of expansion and contraction, often interrupted by mutations that alter both the repeated motif and mutation rate. We applied an empirical, kmer-based, approach to identify genome regions that are likely derived from SSRs.

Results

The sequences flanking annotated SSRs are enriched for similar sequences and for SSRs with similar motifs, suggesting that the evolutionary remains of SSR activity abound in regions near obvious SSRs. Using our previously described P-clouds approach, we identified ‘SSR-clouds’, groups of similar kmers (or ‘oligos’) that are enriched near a training set of unbroken SSR loci, and then used the SSR-clouds to detect likely SSR-derived regions throughout the genome.

Conclusions

Our analysis indicates that the amount of likely SSR-derived sequence in the human genome is 6.77%, over twice as much as previous estimates, including millions of newly identified ancient SSR-derived loci. SSR-clouds identified poly-A sequences adjacent to transposable element termini in over 74% of the oldest class of Alu (roughly, AluJ), validating the sensitivity of the approach. Poly-A’s annotated by SSR-clouds also had a length distribution that was more consistent with their poly-A origins, with mean about 35 bp even in older Alus. This work demonstrates that the high sensitivity provided by SSR-Clouds improves the detection of SSR-derived regions and will enable deeper analysis of how decaying repeats contribute to genome structure.
Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice
Authors: Jury Nur , Abarzua Sebastian , Diaz Ivan , Guerra Miguel V. , Ampuero Estibaliz , Cubillos Paula , Martinez Pablo , Herrera-Soto Andrea , Arredondo Cristian , Rojas Fabiola , Manterola Marcia , Rojas Adriana , Montecino Martín , Varela-Nallar Lorena , van Zundert Brigitte
Published: February 2020

Background

Hexanucleotide repeat expansions of the G4C2 motif in a non-coding region of the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Tissues from C9ALS/FTD patients and from mouse models of ALS show RNA foci, dipeptide-repeat proteins, and notably, widespread alterations in the transcriptome. Epigenetic processes regulate gene expression without changing DNA sequences and therefore could account for the altered transcriptome profiles in C9ALS/FTD; here, we explore whether the critical repressive marks H3K9me2 and H3K9me3 are altered in a recently developed C9ALS/FTD BAC mouse model (C9BAC).

Results

Chromocenters that constitute pericentric constitutive heterochromatin were visualized as DAPI- or Nucblue-dense foci in nuclei. Cultured C9BAC astrocytes exhibited a reduced staining signal for H3K9me3 (but not for H3K9me2) at chromocenters that was accompanied by a marked decline in the global nuclear level of this mark. Similar depletion of H3K9me3 at chromocenters was detected in astrocytes and neurons of the spinal cord, motor cortex, and hippocampus of C9BAC mice. The alterations of H3K9me3 in the hippocampus of C9BAC mice led us to identify previously undetected neuronal loss in CA1, CA3, and dentate gyrus, as well as hippocampal-dependent cognitive deficits.

Conclusions

Our data indicate that a loss of the repressive mark H3K9me3 in astrocytes and neurons in the central nervous system of C9BAC mice represents a signature during neurodegeneration and memory deficit of C9ALS/FTD.
Miller Fisher syndrome with bilateral vocal cord paralysis: a case report
Authors: Ramakrishna Karan N. , Tambe Vikrant , Kattamanchi Adithya , Dhamoon Amit S.
Published: February 2020

Background

Miller Fisher syndrome is a variant of acute inflammatory demyelinating polyneuropathy classically characterized by ataxia, ophthalmoplegia, and areflexia. Miller Fisher syndrome can present with uncommon symptoms such as bulbar, facial, and somatic muscle palsies and micturition disturbance.

Case presentation

We describe the case of a 76-year-old white man with new-onset ataxia, stridor, areflexia, and upper and lower extremity weakness who required intubation at presentation. An initial work-up including imaging studies and serum tests was inconclusive. Eventually, neurophysiological testing and cerebrospinal fluid analysis suggested a diagnosis of Miller Fisher syndrome. Our patient responded to treatment with intravenous immunoglobulin and supportive therapy.

Conclusion

The occurrence of acute or subacute descending paralysis with involvement of bulbar muscles and respiratory failure can often divert clinicians to a diagnosis of neuromuscular junction disorders (such as botulism or myasthenia gravis), vascular causes like stroke, or electrolyte and metabolic abnormalities. Early identification of Miller Fisher syndrome with appropriate testing is essential to prompt treatment and prevention of further, potentially fatal, deterioration.
Some new discrete Hilbert’s inequalities involving Fenchel–Legendre transform
Authors: Hamiaz A. , Abuelela W.
Published: February 2020

Some new Hilbert-type inequalities involving Fenchel–Legendre transform are introduced. These inequalities give more general forms of some previously proved inequalities.
Accelerating the computation for real-time application of the sinc function using graphics processing units
Authors: Kim Sangwoo , Lee Chulhyun
Published: February 2020

In magnetic resonance imaging, the fidelity of image reconstruction is an important criterion. It has been suggested that the infinite-extent sinc kernel is the ideal interpolation kernel for ensuring the reconstruction quality of non-Cartesian trajectories. However, the application of the sinc function has been limited owing to its computational overheads. Recently, graphics processing units (GPUs) have been employed as fast computation tools because of their efficient and versatile parallel computation abilities. We implemented an accelerated convolution function with the sinc kernel using GPUs computing and evaluated the reconstruction performance. The computation time was significantly improved: Computation using the proposed method was approximately 270 times faster than that on a central processing unit (CPU) and approximately 4.6 times faster than that on a CPU optimized by level-3 Basic Linear Algebra Subprograms. The images reconstructed using the fast sinc function exhibited no adverse errors at all matrix sizes (resolutions). The total reconstruction time was approximately 0.3–3 s for all matrices, indicating that the sinc function could be a practical option for image reconstruction. Ultimately, its application would present a fundamental improvement to the performance of image reconstruction, and the GPU implementation of the convolution function with the sinc kernel could resolve various challenges in image data processing.
Pneumatically-driven stretching machine for ankle dorsiflexion: safety concepts and effectiveness test involving healthy young subjects
Authors: Shiraishi Yuma , Okamoto Shogo , Yamada Naomi , Inoue Koki , Akiyama Yasuhiro , Yamada Yoji
Published: February 2020

Stretching is a major treatment for restoring the ankle range of motion while decreasing the ankle stiffness. An automatic stretching machine can provide long-term continual stretching at home. However, no commercial stretching machines are currently available, and therefore, no safety guidelines exist for them. In this study, we prototyped a stretching machine using a chassis from a commercial foot exerciser for preventing disuse syndrome, and then proposed three safety concepts as general requirements for stretching machines. The concepts were determined based on risk assessments, which included (1) preventing excessive force from being applied to the foot, (2) responding to the ankle stiffness and the range of motion of each different individual, and (3) preventing unintended operations by the user. The above concepts allowed us to develop a stretching machine taking into account safety measures. Further, the stretching effect of the prototype was tested on sixteen healthy young subjects ($$22.3 \pm 3.6\hbox { years}$$22.3±3.6years). We found that the passive resistance of the subjects at specific dorsiflexion angles decreased significantly after stretching the ankle using the prototyped machine.
Improved fruit fly algorithm on structural optimization
Authors: Li Yancang , Han Muxuan
Published: February 2020

To improve the efficiency of the structural optimization design in truss calculation, an improved fruit fly optimization algorithm was proposed for truss structure optimization. The fruit fly optimization algorithm was a novel swarm intelligence algorithm. In the standard fruit fly optimization algorithm, it is difficult to solve the high-dimensional nonlinear optimization problem and easy to fall into the local optimum. To overcome the shortcomings of the basic fruit fly optimization algorithm, the immune algorithm self–non-self antigen recognition mechanism and the immune system learn–memory–forgetting knowledge processing mechanism were employed. The improved algorithm was introduced to the structural optimization. Optimization results and comparison with other algorithms show that the stability of improved fruit fly optimization algorithm is apparently improved and the efficiency is obviously remarkable. This study provides a more effective solution to structural optimization problems.
Childhood tuberculosis treatment outcome and its association with HIV co-infection in Ethiopia: a systematic review and meta-analysis
Authors: Belay Getaneh Mulualem , Wubneh Chalachew Adugna
Published: February 2020

Background

Tuberculosis is the second leading cause of death from an infectious disease worldwide, next to HIV. Hence, initiating and determining the national tuberculosis treatment program and outcome is crucial. However, the childhood tuberculosis treatment outcome in Ethiopia was not investigated.

Objective

This study determined the pooled estimate of childhood tuberculosis treatment outcome and its association with HIV co-infection.

Methods

PubMed, Google Scholar, Web of Science, reference lists of included studies, and Ethiopian institutional research repositories were used to retrieve all available studies. Searching was limited to the studies that had been conducted in Ethiopia and published in the English language. In this study, observational studies, including cohort, cross-sectional, and case-control studies, were included. The estimate of childhood tuberculosis treatment outcome was determined using a weighted inverse variance random-effects model. The overall variation between studies was checked by the heterogeneity test (I2). The Joanna Briggs Institute (JBI) quality appraisal criteria were used for quality assessment of the studies. The summary estimates were presented with forest plots and tables. Publication bias was also checked with the funnel plot and Egger’s regression test. The outcome measures were successful and unsuccessful treatment outcomes. Successful treatment outcomes are defined as patients who are cured and treatment completed, whereas, an unsuccessful treatment outcome means those patients with defaulter, failure, and death treatment outcomes.

Result

To estimate the overall pooled estimate of successful treatment outcome, 6 studies with 5389 participants were considered. Consequently, the overall pooled estimate of successful treatment outcome was 79.62% (95% CI 73.22, 86.02) of which 72.44% was treatment completed. On the other hand, unsuccessful treatment outcomes, including treatment failure, defaulter, and death, were 0.15%, 5.36%, and 3.54%, respectively. Moreover, this study found that HIV co-infection was significantly associated with childhood tuberculosis treatment outcomes. Poor treatment outcome was higher among children with HIV co-infection with an odds ratio of 3.15 (95% CI 1.67, 5.94) compared to that of HIV-negative children.

Conclusion

The summary estimate of successful childhood tuberculosis treatment outcome was low compared to the threshold suggested by the World Health Organization. HIV co-infection is significantly associated with poor treatment outcome of childhood tuberculosis. Therefore, special attention is better to be given to children infected with HIV. Moreover, adherence to anti-TB has to be strengthened.

Trial registration

The protocol has been registered in PROSPERO with a registration number of CRD42018110570.
Effect of different plant extracts and nanoparticles on Thrips tabaci (Lind.) (Thysanoptera: Thripidae) under field conditions and their allelopathic potential on the onion, Allium cepa L. using bioassays and RAPD analysis
Authors: Qari Sameer H. , Khalil Abdelhalem H. , Abdelfattah Nilly A. H. , Shehawy Ayman A.
Published: February 2020

The present study was conducted to investigate the toxicity of Aerosil 200® (fumed silica nanoparticles) and leaf extracts of four plants, Cinnamomum camphora, Matricaria chamomilla, Mentha arvensis, and Trigonella foenum-graecum against Thrips tabaci (Lind.) (Thysanoptera: Thripidae) in onion fields, as well their allelopathic effects on onions; moreover, the chlorophyll, phenol, and protein contents were determined in onions. This study was performed in completely randomized plots. After a growth period of 1 month, bioassay investigations and molecular polymorphism in T. tabaci by RAPD-PCR were performed, and total chlorophyll, phenol, and protein concentrations were investigated in onion plants posttreatment as well. The initial reduction% of the T. tabaci population in onion fields after application of a high concentration of nanoparticles (Aerosil 200® (4 ml/l)) and 8000 ppm concentrations of the four plant extracts were 83.66, 81.08, 86.92, 74.49, and 91.38%, respectively, whereas their persistence effects were 73.18, 67.78, 71.46, 66.94, and 78.29%, respectively. Furthermore, the total chlorophyll contents in onions treated with the nanoparticles and four plant extracts were 1.35, 1.17, 1.09, 1.07, and 1.18 mg/g, respectively; additionally, the concentrations of phenols were 4.65, 3.15, 3.15, 2.85, and 3.70 mg/g in onions treated with C. camphora, M. chamomilla, M. arvensis, T. foenum-graecum, and Aerosil 200®, respectively. The C. camphora extract was the most potent, as it increased the protein content in the onion plants, while the Aerosil 200® decreased the protein content in onions. In addition, DNA-RAPD showed that the polymorphism percentages were 73, 71, and 67% when treated with high concentrations of C. camphora and M. arvensis extracts and Aerosol 200®, respectively. T. foenum-graecum and M. chamomilla extracts induced the least polymorphism (17 and 16%, respectively). Overall, this study indicated that these plant extracts as well as the nanoparticles in Aerosil 200® could be used to reduce onion infestations of T. tabaci in the field environment.
Challenges of implementation of hospital accreditation in Iran: an exploratory factor analysis
Authors: Tashayoei Narges , Raeissi Pouran , Nasiripour Amir Ashkan
Published: February 2020

Background

Today, accreditation is considered as the most commonly used health assessment approach. Considering the importance and application of the process of this approach in the hospital, this study aimed to investigate the challenges of implementation of hospital accreditation in Iran using exploratory factor analysis.

Methods

A cross-sectional study design was carried out from July to December 2017, consisting of 200 managers in the seven hospitals accredited by the MOH in Tehran, Iran. Samples were selected through the purposive sampling method, and data were collected using a structured questionnaire in which validity and reliability were confirmed. Likert’s five-choice range was used for the rating of items. Exploratory factor analysis was used to categorize the identified challenges and extract the mathematical model on them.

Results

Exploratory factor analysis identified six dimensions (implementation, evaluation, content, structural, psychological, and managerial) with 40 items using a 5-point Likert scale. Each dimension accounted for greater than 63.20% of the total variance. The scale had strong content validity (indices = 0.84). Each dimension of Cronbach’s alpha ranged from 0.74 to 0.94. Implementation, evaluation, content, structural, psychological, and managerial components also formed the final identified areas.

Conclusion

The present study showed that there were major challenges in the path to successful deployment of Iranian hospital accreditation, requiring serious action by managers and policymakers in this field.
Demographic transition in Sultanate of Oman: emerging demographic dividend and challenges
Authors: Islam M. Mazharul
Published: February 2020

Background

The sharp fall in fertility and mortality in Oman in recent time is quite stunning and more than expected, which is largely remained unexplored. This paper examined the characteristics of demographic changes and the emerging windows of opportunities and challenges for Oman. It also discussed the policy options. Data come from the national level surveys and censuses as well as the World Population Prospects 2019 Revision of the United Nations.

Results

The population of Oman grew from less than half a million in 1950 to more than four million in 2015, and expected to reach to seven million by 2055. After 1970, the annual growth rate of population accelerated due to increased immigration of working age population which has increased from less than 1% in 1970 to 44% in 2015. The fertility rate has declined from 8.6 births per woman in 1988 to 3.3 births per woman in 2008, a decline of 5.3 births per woman or 62% decline within a short period of 20 years. Under-five mortality also declined from 359 deaths per 1000 live births in 1950 to nine deaths per 1000 live births in 2015. Demographic transitions leads to many changes in the size and age structure of the population in Oman that open up the opportunities of accruing demographic dividend for economic development of the country. The dependency ratio has decreased from 98% in 1970 to 32% in 2015. Two opening of demographic dividend period has been observed—first from 1958 to 2000 and the second one has opened in 2010 which will reach its peak during the 2020s and will remain open until 2040.

Conclusion

Oman has been experiencing a period of youth bulge over the years and it is expected to continue for at least next 20 years. To reap the benefits of the emerged demographic dividend, necessary steps need to be taken in a timely manner to develop human resources. Understanding the demographic challenges must be a priority for the government of Oman, and formulate policies to harvest the benefits of the demographic windows.
Laparoscopic gastrectomy with D2 lymphadenectomy for gastric cancer: initial Egyptian experience at the National Cancer Institute
Authors: Abdelhamed Mohamed Aly , Abdellatif Ahmed , Touny Ahmed , Mahmoud Ahmed Mostafa , Ahmed Ihab Saad , Maamoun Sherif , Shalaby Mohamed
Published: February 2020

Background

Laparoscopic gastrectomy has been used as a superior alternative to open gastrectomy for the treatment of early gastric cancer. However, the application of laparoscopic D2 lymphadenectomy remains controversial. This study aimed to evaluate the feasibility and outcomes of laparoscopic gastrectomy with D2 lymphadenectomy for gastric cancer.

Results

Between May 2016 and May 2018, twenty-five consecutive patients with gastric cancer underwent laparoscopic D2 gastrectomy: eighteen patients (72%) underwent distal gastrectomy, four patients (16%) underwent total gastrectomy, and three patients (12%) underwent proximal gastrectomy. The median number of lymph nodes retrieved was 18 (5–35). A positive proximal margin was detected in 2 patients (8%). The median operative time and amount of blood loss were 240 min (200–330) and 250 ml (200–450), respectively. Conversion to an open procedure was performed in seven patients (28%). The median hospital stay period was 8 days (6–30), and the median time to start oral fluids was 4 days (3–30). Postoperative complications were detected in 4 patients (16%). There were two cases of mortality (8%) in the postoperative period, and two patients required reoperation (8%).

Conclusions

Laparoscopic gastrectomy with D2 lymphadenectomy can be carried out safely and in accordance with oncologic principles.
Transpleural versus extrapleural approach in treatment of esophageal atresia
Authors: Batikhe Mohamed
Published: February 2020

Background

Surgery is the only curative treatment of patients with esophageal atresia and tracheoesophageal fistula. A lot of surgeons recommend transpleural repair while others prefer extrapleural approach for repair. This study will evaluate the differences, advantages, outcome, and the disadvantages of the two techniques.

Results

Duration of surgery was significantly shorter in the group operated by transpleural approach. The incidence of pneumothorax was higher in patients operated by transpleural approach.

Conclusion

Operating esophageal atresia and tracheoesophageal fistula by transpleural approach has significantly shorter time of surgery, but there is no difference between the two groups as regards incidence of leakage or mortality.
Plasma Glycated CD59 Predicts Early Gestational Diabetes and Large for Gestational Age Newborns
Authors: Ma DongDong , Luque-Fernandez Miguel Angel , Bogdanet Delia , Desoye Gernot , Dunne Fidelma , Halperin Jose A
Published: February 2020

Context

Gestational diabetes mellitus (GDM) diagnosed in early pregnancy is a health care challenge because it increases the risk of adverse outcomes. Plasma-glycated CD59 (pGCD59) is an emerging biomarker for diabetes and GDM. The aim of this study was to assess the performance of pGCD59 as a biomarker of early GDM and its association with delivering a large for gestational age (LGA) infant.

Objectives

To assess the performance of pGCD59 to identify women with GDM in early pregnancy (GDM < 20) and assess the association of pGCD59 with LGA and potentially others adverse neonatal outcomes linked to GDM.

Methods

Blood levels of pGCD59 were measured in samples from 693 obese women (body mass index > 29) undergoing a 75-g, 2-hour oral glucose tolerance test (OGTT) at <20 weeks’ gestation in the Vitamin D and Lifestyle Intervention study: the main analyses included 486 subjects who had normal glucose tolerance throughout the pregnancy, 207 who met criteria for GDM at <20 weeks, and 77 diagnosed with GDM at pregnancy weeks 24 through 28. Reference tests were 75-g, 2-hour OGTT adjudicated based on International Association of Diabetes and Pregnancy Study Group criteria. The index test was a pGCD59 ELISA.

Results

Mean pGCD59 levels were significantly higher (P < 0.001) in women with GDM < 20 (3.9 ± 1.1 standard peptide units [SPU]) than in those without (2.7 ± 0.7 SPU). pGCD59 accurately identified GDM in early pregnancy with an area under the curve receiver operating characteristic curves of 0.86 (95% confidence interval [CI], 0.83-0.90). One-unit increase in maternal pGCD59 level was associated with 36% increased odds of delivering an LGA infant (odds ratio for LGA vs non-LGA infant: 1.4; 95% CI, 1.1-1.8; P = 0.016).

Conclusion

Our results indicate that pGCD59 is a simple and accurate biomarker for detection of GDM in early pregnancy and risk assessment of LGA.
IDH1 Expression via the R132H Mutation–Specific Antibody in Adrenocortical Neoplasias—Prognostic Impact in Carcinomas
Authors: Pennanen Mirkka , Tynninen Olli , Kytölä Soili , Ellonen Pekka , Mustonen Harri , Heiskanen Ilkka , Haglund Caj , Arola Johanna
Published: February 2020

Context

Mutations to isocitrate dehydrogenase (IDH) appear to play a prognostic or predictive role in several neoplasias. Immunohistochemical staining designed to detect a specific R132H mutation to IDH1 showed expression in the normal adrenal cortex, raising interest to study the potential role of IDH1 in the pathogenesis of adrenocortical tumors.

Objective

The objective of this work is to study the role of IDH1 and its mutations in adrenocortical tumors.

Design and patients

IDH1 R132H immunohistological staining was performed on a cohort of 197 adrenocortical tumors. The exon of the IDH1 gene was sequenced in 16 tumors.

Results

Positive IDH1 R132H immunohistochemical staining correlated with a better prognosis among patients with a malignant adrenocortical tumor. However, IDH1 R132H immunohistochemistry did not distinguish between local and metastasized tumors. We were unable to identify IDH1 mutations among our adrenocortical tumors using a targeted next-generation sequencing panel or via exon sequencing.

Conclusions

Among adrenocortical carcinomas, IDH1 R132H immunopositivity correlated with a better prognosis. Thus, IDH1 R132H immunohistochemical staining could serve as a prognostic or as a potential predictive marker in adrenocortical carcinomas. Further research is needed to identify the possible alterations in IDH1 that could explain our findings, because we identified no known mutations to the IDH1 gene.
Association of systemic lupus erythematosus disease activity index score with clinical and laboratory parameters in pediatric onset systemic lupus erythematosus
Authors: Shamim Roshila , Farman Sumaira , Batool Shabnam , Anwer Khan Saira Elaine , Raja Muhammad Kamil Hussain
Published: February 2020

Objective: To determine the association of systemic lupus erythematosus disease activity index (SLEDAI) score in pediatric onset SLE (p-SLE) with clinical and laboratory parameters.

Methods: This cross sectional observational study was conducted at Division of Rheumatology, Fatima Memorial Hospital, Lahore from November 2018 to January 2019. Total 23 patients diagnosed with p-SLE having onset of symptoms at ≤ 18 years of age, irrespective of their current age at presentation, of either gender, fulfilling criteria of 2012 Systemic Lupus International Collaborating Clinics (SLICC) criteria were enrolled. Patients’ clinical symptoms and laboratory parameters were reviewed, SLEDAI scores were calculated. Collected Data were entered in proforma and analyzed on SPSS version 23.

Results: There were 91.3% females. Mean age at diagnosis was 11years ± 4years. At presentation patients had hematological involvement 69.6% followed by mucocutaneous symptoms 65.2% and renal involvement 21.6%. ANA by IFA was positive in all, while anti-ds-DNA was positive in 78.3% patients. SLEDAI score was ≥6 in 87% patients, average SLEDAI score was higher in patients with renal involvement (p=0.06). Elevated ESR (r=0.48, p=0.02), Anti-dsDNA (r=0.44, p=0.05) and low complement levels (p=0.03) were significantly positively correlated, while hemoglobin (r= -0.43, p=0.04) was negatively correlated with the SLEDAI score.

Conclusion: In this study, patients with Lupus Nephritis had high SLEDAI scores. Elevated Anti-dsDNA titer, ESR, low complement levels and hemoglobin were significantly associated with high SLEDAI scores. We recommend that SLEDAI score should be calculated in p-SLE patients for stringent disease monitoring and treatment.

doi: https://doi.org/10.12669/pjms.36.3.1480

How to cite this:Shamim R, Farman S, Batool S, Khan SEA, Raja MKH. Association of systemic lupus erythematosus disease activity index score with clinical and laboratory parameters in pediatric onset systemic lupus erythematosus. Pak J Med Sci. 2020;36(3):467-472.  doi: https://doi.org/10.12669/pjms.36.3.1480

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Blended Learning: The impact of blackboard formative assessment on the final marks and students’ perception of its effectiveness
Authors: Baig Mukhtiar , Gazzaz Zohair Jamil , Farooq Mohamed
Published: February 2020

Objective: To explore the impact of Blackboard (Bb) formative assessment on the final score in the endocrine module and determine the medical students’ perception of the impact and effectiveness of Bb.

Methods: This exploratory case study was carried out at the King Abdulaziz University (KAU), Jeddah, Saudi Arabia (SA). Blackboard was used in the course management and formative assessment of third-year medical students and three years of data was collected (2016, 2017, 2019). In the last week of the module before the final exam, a formative assessment test that comprised of 50 Multiple Choice Questions (MCQs) was posted on Bb each year. All the students filled a questionnaire regarding their perception about the impact and effectiveness of Bb.

Results: Overall, summative exam scores were significantly higher than the scores in formative assessment (p <0.001). A substantial positive correlation was observed between students’ marks in the online (Bb) MCQ exam and their final exam marks (p <0.001). Regarding the features of Bb, most often used by the students’ were course resources uploaded on the Bb, assignments, online quizzes, and others. Majority of the students were satisfied with the use of Bb in this module.

Conclusions: The majority of the students liked this blended learning (BL) method and conceded the impact and effectiveness of Bb. The formative online assessment on Bb improved the students’ performance in the final exam and a positive correlation was noted between students’ marks in online (Bb) exams with their final exam marks.

doi: https://doi.org/10.12669/pjms.36.3.1925

How to cite this:Baig M, Gazzaz ZJ, Farouq M. Blended Learning: The impact of blackboard formative assessment on the final marks and students’ perception of its effectiveness. Pak J Med Sci. 2020;36(3):327-332. doi: https://doi.org/10.12669/pjms.36.3.1925

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Ecological and geological problems of development of oil and gas fields in the Caspian region
Authors: Serebryakov Oleg
Published: February 2020

The paper summarizes and examined extensive evidence on the environmental, geological and technological challenges of exploration and production of oil and gas, encountered during the development of the gigantic fields. Investigated environmental problems of underground disposal of wastes, the formation of zones of technogenic pollution, ecology megalonyx pressures and many others. Describes the environmental effects of oil and gas companies on the environment. The proposal for reducing the negative anthropogenic influence on the geoecological conditions of the environment. Justified the monitoring of the exploration and exploitation of deposits of natural raw materials.
Is designed to masters, post-graduate students and students studying on the specialty "Environmental Geology", "Geology and Geochemistry of combustible minerals", "Geology of marine oil and gas fields", "Hydrogeology and engineering Geology", a wide range of scientific and industrial workers of the oil and gas industry, high school teachers and graduate students geoenvironmental, environmental, oil and gas fields.
Economic and mathematical and econometric modeling: Computer workshop
Authors: Kolpakov Vasiliy
Published: February 2020

The textbook presents mathematical research methods and models of economic objects and processes designed for the analysis and prediction of economic factors and develop control solutions as in the deterministic conditions, and in conditions of some uncertainty, and dynamics. Each Chapter of the book consists of a theoretical framework, discussed in detail several examples and tasks for independent work. As workbench simulation uses standard office the program Excel and Mathcad. Tutorial focused on independent performance of students individual tasks on disciplines "Economic-mathematical methods" and "Econometrics".
Meets the requirements of Federal state educational standard of higher education of the last generation.
The publication is intended for students and postgraduate students in economic disciplines. It can also be useful as they perform final qualifying works. The book will be useful for practitioners engaged in the analysis of the current financial and economic condition and future development of firms and businesses.
Russia, Euroasian economic union and World Trade Organization
Authors: Kashirkina Anna , Morozov Andrey
Published: February 2020

The monograph is the first scientific publication, considering the complex
international legal issues of the integration of rapprochement of the Russian
Federation, Belarus and Kazakhstan after the signing of the Heads of State May
29, 2014 the Treaty on the Eurasian Economic Union. The monograph is held
international legal analysis of the contractual framework prior Eurasian Economic
Union integration union – Customs Union. The position of the new interstate
integration association – the Eurasian Economic Union – as a subject of public
international law. On the basis of comparative legal analysis mapped international
legal obligations, operating under the World Trade Organization, as well as the
provisions of the Treaty on the Eurasian Economic Union, including in the areas
of customs regulation, industrial policies, and technical regulation. Give
suggestions and recommendations for improving and promoting the integration
of the former Soviet Union in the framework of the Eurasian Economic Union,
taking into account Russia’s membership in the World Trade Organization, as well
as the possible accession by the Republic of Belarus and the Republic of
Kazakhstan – Russia’s partners in the Eurasian Economic Union.
The monograph focuses on a wide range of readers: researchers and experts
in the field of international law and international relations, employees of public
authorities, business representatives, teachers and law faculties, graduate students,
and all interested in the integration of the modern world.
Improving fluid consumption of older people in care homes: an exploration of the factors contributing to under-hydration
Authors: Wilson Jennie , Tingle Alison , Bak Aggie , Greene Carolynn , Tsiami Amalia , Loveday Heather
Published: February 2020

Age-related changes put older people at risk of dehydration, and care home residents are particularly vulnerable. Researchers at the University of West London outline their study that identifies the possible barriers and facilitators to optimising hydration in nursing homes, offering guidance for service improvement initiatives
Singular Values, Eigenvalues and Diagonal Elements Of The Commutator Of 2x2 Rank One Matrices
Authors: Cheng Che-Man , Liang Yaru
Published: February 2020

We determine the region of singular values of the commutator XY-YX for 2x2 rank one complex matrices X and Y. This answers in affirmative a conjecture raised in [Wenzel 2015] when 2x2 matrices are concerned. Our approach and proofs also lead to a complete relation between the singular values, eigenvalues and diagonal elements of the commutator under consideration.
Tellurium as the saturable absorber for the passively Q-switched laser at 1.34 µm
Authors: Yang Qi , Zhang Xiaoyan , Yang Zixin , Ren Xianghe , Nie Hunkun , Yan Bingzheng , Yang Kejian , Zhang Baitao , He Jingliang , Wang Jun
Published: February 2020

The novel two-dimensional (2D) elementary tellurium is currently of great interest in optoelectronic and photonic applications. In this contribution, 2D tellurium nanosheets were successfully created by using the liquid-phase exfoliation method. With the as-prepared tellurium nanosheets as the saturable absorber (SA), we realized a passively

Q

-switched

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d

:

Y
V
O

4

laser operating at 1342 nm with a pulse width of 947 ns and single pulse energy of 2.25 µJ. Our work indicated the tellurium SA could be an efficient

Q

-switcher for a near-infrared solid-state laser.
Color quality evaluation of Chinese bronzeware in typical museum lighting
Authors: Huang Zheng , Liu Qiang , Pointer Michael R. , Chen Wei , Liu Ying , Wang Yu
Published: February 2020

A series of psychophysical experiments have been conducted to investigate the effect of light sources on the color appearance of Chinese bronzeware. Three groups of 30 observers were asked to evaluate a set of Chinese bronzeware under different light sources in three paired-comparison experiments—one group of observers for each experiment. The visual attributes of color preference, color comfort, color discrimination, and antiquity were scaled. A panel of seven light sources of 3000 K, with Duv values ranging from

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0

.

015

to 0.015, was used in Experiment 1. A second panel of seven light sources of 4000 K, with a similar range of Duv values, was used in Experiment 2. For Experiment 3, six light sources were chosen from Exps. 1 and 2, plus four lights of 2700 K, 3300 K, 3700 K, and 4300 K, with Duv values of zero. These experimental lights produced a constant illuminance of approximately 200 lux in a pair of viewing booths, and their color rendering indices were between 88 and 95. The results showed that the subjective judgments for color preference and color comfort were highly correlated while the whiteness of the lighting strongly influenced the perception of color preference, comfort, and discrimination. A light source of 4000 K with a Duv value of zero exhibited the best color preference and color comfort performance, while observers were found to show the greatest capability for color discrimination under a light source of 4000 K with a Duv value of

−

0

.

015

. In addition, the bronzeware appeared to have greatest antiquity when illuminated by a 3000 K light source with a Duv value equal to 0.005. Based on the psychophysical data, the performance of typical color quality metrics were also tested in relation to the four scaled visual attributes.
Hue selectivity of collinear facilitation
Authors: Sato Tomoharu , Nagai Takehiro , Kuriki Ichiro
Published: February 2020

Collinear facilitation (CF) is the improvement of the detection
sensitivity of the target when two high-contrast flanking stimuli
(flankers) have the same visual properties. While it is known that CF
does not occur between achromatic flanking stimuli and chromatic
targets, or vice versa, it remains unclear whether CF occurs when the
hue of the target and flankers are different. We measured CF for Gabor
stimuli defined in an isoluminant plane using stimuli defined by
isoluminant colors along isolated cone-opponent axes and in two
diagonal directions. The measured CF varied with the difference in hue
between the target and flankers. Moreover, increased thresholds were
also observed. These results suggest that CF exhibits hue selectivity
and involves a suppression as well as a facilitation component. The
hue selectivity profile of these factors infer that the CF cannot be
simply explained by the assumption of two independent cone opponent
mechanisms.
Broadband directional rhombic nanoantenna for optical wireless communications systems
Authors: Elsaid Mohamed , Mahmoud Korany R. , Hameed Mohamed Farhat O. , Obayya S. S. A. , Hussein Mohamed
Published: February 2020

In this paper, an optimized four-nanowire rhombic nanoantenna (RNA) is proposed and numerically analyzed in terms of directivity and efficiency. The suggested design achieves a directivity of 23.4 with 84.5% radiation efficiency at a wavelength of 1550 nm. Further, the suggested nanoantenna (NA) design offers a high gain of 18.5 with an enhancement of 172%, compared to the previously reported plasmonic horn NA. Additionally, the wireless transmission power of the nanolink based on the optimized rhombic design is analyzed. The numerical results reveal that the RNA enjoys a much lower loss by 32 dB and 12 dB, respectively, when compared to the dipole and plasmonic horn NAs. Moreover, the reported design has broadband operation features over the optical C-band range, making it a promising candidate for applications related to optical communications nanochips.
Improved localization algorithm for distributed fiber-optic sensor based on merged Michelson-Sagnac interferometer
Authors: Song Qiuheng , Zhou Pengwei , Peng Hekuo , Hu Yuhan , Xiao Qian , Wu Hongyan , Jia Bo
Published: February 2020

A novel distributed fiber-optic localization algorithm with high sensitivity and precision based on merged Michelson-Sagnac interferometer is proposed and demonstrated. By performing simple addition and subtraction processing on the two phase differences of the two interferometers, two superimposed signals with a fixed delay can be obtained. The time delay can be calculated by a cross-correlation algorithm. Combined with the polynomial fitting interpolation, the disturbance location resolution is significantly improved. The total sensing distance can reach 120 km, and the localization errors are within ±35 m and ±160 m in the contact and non-contact disturbance experiment, respectively.
Photophysics of quantum emitters in hexagonal boron-nitride nano-flakes
Authors: Boll Mads K. , Radko Ilya P. , Huck Alexander , Andersen Ulrik L.
Published: February 2020

Quantum emitters in hexagonal boron nitride (hBN) have attracted significant interest due to their bright and narrowband photon emission even at room temperature. The wide-bandgap two-dimensional material incorporates crystal defects of yet-unknown configuration, introducing discrete energy levels with radiative transition frequencies in the visible spectral range. The commonly observed high brightness together with the moderate fluorescence lifetime indicates a high quantum efficiency, but the exact dynamics and the underlying energy level structure remain elusive. In this study we present a systematic and detailed analysis of the photon statistics recorded for several individual emitters. We extract the individual decay rates by modeling the second-order correlation functions using a set of rate equations based on an energy level scheme involving long-lived states. Our analysis clearly indicates excitation-power-dependent non-radiative couplings to at least two metastable levels and confirms a near unity quantum efficiency.
Fully refractive adaptive optics fluorescence microscope using an optofluidic wavefront modulator
Authors: Rajaeipour Pouya , Dorn Alex , Banerjee Kaustubh , Zappe Hans , Ataman Çağlar
Published: February 2020

Adaptive optics (AO) represents a powerful range of image correction technologies with proven benefits for many life-science microscopy methods. However, the complexity of adding a reflective wavefront modulator and in some cases a wavefront sensor into an already complicated microscope has made AO prohibitive for its widespread adaptation in microscopy systems. We present here the design and performance of a compact fluorescence microscope using a fully refractive optofluidic wavefront modulator, yielding imaging performance on par with that of conventional deformable mirrors, both in correction fidelity and articulation. We combine this device with a modal sensorless wavefront estimation algorithm that uses spatial frequency content of acquired images as a quality metric and thereby demonstrate a completely in-line adaptive optics microscope that can perform aberration correction up to 4
th
radial order of Zernike modes. This entirely new concept for adaptive optics microscopy may prove to extend the performance limits and widespread applicability of AO in life-science imaging.
Design of spherical aberration free liquid-filled cylindrical zoom lenses over a wide focal length range based on ZEMAX
Authors: Sun Licun , Sheng Shuwu , Meng Weidong , Wang Yuanfangzhou , Ou Quanhong , Pu Xiaoyun
Published: February 2020

A systematic design idea for liquid-filled cylindrical zoom lenses with ideal imaging quality over a wide focal length range is introduced in detail. The PWC method is used to calculate the initial structure parameters of the zoom lenses, and the optical design software ZEMAX is used to eliminate the spherical aberration at different focal lengths. Lenses named SLCL-Doublet are finally designed, which are formed by a symmetric liquid-core cylindrical lens (SLCL) filled with variable refractive index (RI) liquid and a doublet cylindrical lens capable of significantly weakening the spherical aberration. The focal length of the SLCL-Doublet continuously decreases from 101.406 mm to 54.162 mm as the liquid RI changes from 1.3300 to 1.5000. Calculated over 75% of the full aperture, the root mean square (RMS) spot radius of the SLCL-Doublet is always less than 7 µm over the whole focal length range, and the peak-to-valley wavefront error remains below the λ/4 limit when the focal length ranges from 62.373 mm to 65.814 mm, within which the lenses approach the diffraction limit, demonstrating improvement in the optical performance over that of previously designed liquid-core cylindrical lenses. The sources of potential fabrication and installation errors in the practical implementation of the SLCL-Doublet are also analyzed in detail. The SLCL-Doublet is demonstrated to be characterized by high imaging quality and easy installation, which enriches the types of core optical element for measuring the liquid RI and liquid diffusion coefficient and provides guarantee for improving the measurement accuracy.
Scattering of light by a large, densely packed agglomerate of small silica spheres
Authors: Väisänen T. , Markkanen J. , Hadamcik E. , Renard J.-B. , Lasue J. , Levasseur-Regourd A. C. , Blum J. , Muinonen K.
Published: February 2020

We model the measured phase function and degree of linear polarization of a macroscopic agglomerate made of micrometer-scale silica spheres using the methodology of multiple scattering. In the laboratory work, the agglomerate is produced ballistically, characterized by scanning electron microscopy, and measured with the

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instrument to obtain the light scattering properties. The model phase function and degree of polarization are in satisfactory agreement with the experimental data. To our best knowledge, this is the first time the degree of linear polarization has been modeled well for a large, densely packed agglomerate composed of small particles with known sizes and shapes. The study emphasizes the relevance of the degree of linear polarization and gives insights into the effects of particle aggregation on the scattering characteristics.
Controlling light emission by engineering atomic geometries in silicon photonics
Authors: Nandi Arindam , Jiang Xiaodong , Pak Dongmin , Perry Daniel , Han Kyunghun , Bielejec Edward S. , Xuan Yi , Hosseini Mahdi
Published: February 2020

By engineering atomic geometries composed of nearly 1000 atomic segments embedded in micro-resonators, we observe Bragg resonances induced by the atomic lattice at the telecommunication wavelength. The geometrical arrangement of erbium atoms into a lattice inside a silicon nitride (SiN) microring resonator reduces the scattering loss at a wavelength commensurate with the lattice. We confirm dependency of light emission to the atomic positions and lattice spacing and also observe Fano interference between resonant modes in the system.