bluuebunny/crossref_metadata_2025 huggingface dataset:
CONCEPTION OF LEARNING PHYSICS AND SELF-EFFICACY AMONG INDONESIAN UNIVERSITY STUDENTS
Authors: Suprapto Nadi , Chang Te-Sheng , Ku Chih-Hsiung
Published: August 2021

This research aimed to explore the correlation between Indonesian University students’ conception of learning physics and their physics’ self-efficacy. A total of 279 students who were majoring in physics education participated in this research and were invited to complete two instruments: the conception of learning physics (CLP) and the physics learning’ self-efficacy (PLSE). Both of the questionnaires, which were modified from [Lin, Liang, & Tsai (2015a) and Lin, Liang, & Tsai (2015b)]’ instruments, had been translated into Indonesian language and validated through an exploratory factor analysis of participants’ responses. The differences between student levels were explored for their significance using an ANOVA test in order to portray a clear line among different conceptions of learning physics and physics learning self-efficacy. The results indicated that, first, the instruments used in the research had satisfactory validity and reliability. Second, students in sophomore level were significantly lower on the conceptions of testing than those in other levels. Meanwhile, the conceptions of calculating-practicing and understanding were not significantly different. Third, university students in senior level performed more confident in four dimensions: science content, higher-order thinking, everyday application, and science communication than others. The research also depicted a moderate correlation among dimensions of CLP and PLSE.
Key words: conception of learning, physics education, self-efficacy, survey study, university student.
Evaluación de la fertilidad química del suelo en un sistema inicial productivo de Theobroma cacao de la finca “Hermanos Briones”, Portoviejo - Ecuador
Authors: Briones García Javier Ignacio , Mejía Reinoso Teresita Jackelin , Briones García Huber David
Published: August 2021

Introducción. El suelo es el recurso natural más importante y la mayor parte de la vida en la tierra depende de este, su composición química varia constantemente, dando como resultado un sinnúmero de suelos.  El uso de fertilizantes N, P, K, Ca y Mg se ha vuelto indispensable en la mayoría de suelos con el fin de obtener altos rendimientos y una buena calidad en el producto siendo indispensable monitorear constantemente el suelo en donde se desarrollan los cultivos.  Los rendimientos en la producción de cacao dependen del suelo y de ciertos factores del medio ambiente como son luminosidad, temperatura y humedad. No podrán alcanzarse rendimientos halagadores cuando a pesar del ambiente adecuado los servicios que proporcione el suelo no sean los adecuados (Pinargote, 2010). Objetivo. Evaluar la fertilidad química del suelo en este sistema inicial productivo de Theobroma cacao, en la finca “Hermanos Briones” en el cantón Portoviejo. Metodología. El trabajo de investigación se realizó en un lote agrícola de un cultivo inicial de cacao de 2 años de 2.4 ha, la plantación de cacao utilizada corresponde al clon CCN-51, los muestreos del suelo se realizaron al azar en forma sistemática (zig-zag), obteniendo una muestra compuesta,  para realizar los análisis químicos en laboratorio, dados análisis se realizaron previo a la plantación y a los 2 años del cultivo. Resultados. Se observa la comparación del contenido nutricional del suelo, con respecto a la materia orgánica existe un incremento conforme va creciendo la plantación el desarrollo de materia orgánica es mayor. Los macronutrientes Nitrógeno y Potasio presentan un ligero descenso lo contrario al Fosforo, los mesonutrientes Calcio, Magnesio y Azufre se encuentran en menores cantidades, los micronutrientes Zinc y Cobre presentan un aumento, diferente al Hierro y Boro que a los 2 años de las plántulas ha disminuido las concentraciones de estos elementos en el suelo, con respecto al Manganeso la concentración no ha variado. Conclusiones. Según los resultados del muestreo, el sistema inicial productivo presenta desbalances nutricionales y deficiencias en contenidos de nutrientes para su desarrollo, por lo cual se requiere de planes de fertilización que garanticen una adecuada sostenibilidad del sistema.
Long-term Analysis of Surgically Induced Astigmatism after Combined Vitrectomy and Cataract Surgery versus Cataract Surgery Alone
Authors: Byun Zee Yoon , Lee Jung Hyun , Lee Sang-Mok , Hwang Daniel Duck-Jin
Published: August 2021

Purpose: To compare the long-term changes in surgically induced astigmatism (SIA) in patients who underwent 23-gauge sutureless vitrectomy and cataract surgery together with patients who underwent cataract surgery only.Methods: We retrospectively reviewed SIA changes for 1 year after surgery in patients who received only cataract surgery using phacoemulsification (group 1) and patients who underwent 23-gauge sutureless vitrectomy and cataract surgery together (group 2). Flat keratometry (K1), steep keratometry (K2), and astigmatism axis were measured with automatic keratometry before and after the surgery. Vector analysis was used to calculate SIA at 1, 3, 6, and 12 months postoperatively. We then examined whether the SIA values at each time point were different between the two groups.Results: A total of 86 eyes were included in this study (group 1, n = 45; group 2, n = 41). The mean SIA values calculated at 1, 3, 6, and 12 months after surgery in group 1 were 0.83 ± 0.37, 0.69 ± 0.39, 0.60 ± 0.33, and 0.59 ± 0.33, respectively. In group 2, the values were 0.82 ± 0.47, 0.69 ± 0.38, 0.62 ± 0.28, and 0.61 ± 0.30, respectively. Over time, SIA decreased in both groups (all p < 0.001). There was no significant difference in the mean SIA between the two groups at each follow-up time point after surgery (p = 0.296, p = 0.728, p = 0.361, and p = 0.356, respectively).Conclusions: When 23-gauge sutureless vitrectomy and cataract surgery were performed together, the astigmatism change caused by surgery did not show a significant difference compared with that of the group who received cataract surgery only. Thus, 23-gauge sutureless vitrectomy may not significantly affect corneal astigmatism.
Incidence and Risk Factors of Epiretinal Membrane after Cataract Surgery
Authors: Kim Jae-Ik , Oh Jong-Hyun
Published: August 2021

Purpose: To investigate the incidence and risk factors of epiretinal membrane (ERM) after cataract surgery.Methods: We reviewed the medical records of patients who underwent cataract surgery between January 2016 and December 2018. Eyes with ERM, as observed by optical coherence tomography performed 1-2 months after surgery, were excluded from the study. ERM was diagnosed by fundus photography. The incidence rate was determined 2-6, 6-12, and 12-24 months after surgery. The cumulative incidence rate of ERM was calculated by Kaplan-Meier analysis. Data were analyzed using logistic regression to determine the associations between ERM development and various factors.Results: The study included 218 eyes of 161 patients with a mean age of 66.6 ± 9.7 years at the time of surgery. ERM was observed in 3 of 218 eyes (1.4%) between 2 and 6 months, 15 of 176 eyes (8.3%) between 6 and 12 months, and 14 of 150 eyes (10.3%) between 12 and 24 months after surgery. The cumulative incidence rate of ERM was 11.7% over the 24-month period after surgery. In multivariate logistic regression analysis, older age (≥65 years; odds ratio [OR], 8.59, 95% confidence interval [CI], 1.43-51.49), fellow eye with ERM (OR, 3.63; 95% CI, 1.04-12.73), longer axial length (≥26 mm; OR, 8.02; 95% CI, 1.08-59.66), and complete posterior vitreous detachment development (OR, 7.48; 95% CI, 1.64-34.14) were significantly associated with ERM development.Conclusions: ERM is not rare after cataract surgery. Long-term retinal examination should be required after cataract surgery.
Depression, Anxiety, Somatization Disorder, and Adjustment Disorder in Older Patients with Exudative Age-related Macular Degeneration
Authors: Lee Hee Chul , Nam Hyewon , Kang Dongwoo , Yeom Myeong In
Published: August 2021

Purpose: The aim of this study was to analyze the prevalence of depression, anxiety, somatization disorder, and adjustment disorder in older patients diagnosed with exudative age-related macular degeneration (AMD) and to evaluate the relationship between exudative AMD and psychological disease.Methods: The 2016 Health Insurance Review and Assessment Service-Aged Patient Sample was applied in this study. The subjects were divided into two groups: AMD patients undergoing intravitreal injection treatment and a control group. Comorbidities were evaluated using the Charlson Comorbidity Index.Results: A total of 1,319,052 subjects were selected, of which 3,134 were in the exudative AMD group receiving intravitreal injections. The average age of the subjects was 74.7 ± 6.7 years, and 41.8% were male. In patients with exudative AMD, the prevalence of depression, anxiety, somatization disorder, and adjustment disorder were 16%, 20%, 0.5%, and 0.4%, respectively; in particular, the prevalence of depression and adjustment disorder were significantly higher than in the control group. In multivariate regression analysis, exudative AMD was a significant factor of depression (odds ratio [OR] 1.2, 95% confidence interval [CI] 1.08-1.31, p < 0.001) and adjustment disorder (OR 2.47, 95% CI 1.47-4.18, p < 0.001). However, the association between AMD and anxiety or somatization disorder was not statistically significant.Conclusions: Exudative AMD showed a significant association with psychiatric disease, such as depression, and requires close clinical attention.
Long-term Clinical Course of Korean Patients Diagnosed with Macular Telangiectasia Type 2
Authors: Kang Kyung Hae , Yoon Ji Hyun , Kim Jong Woo , Kim Chul Gu , Kim Jae Hui
Published: August 2021

Purpose: To evaluate long-term visual prognosis and changes in the retinal microstructure in patients with macular telangiectasia type 2.Methods: Retrospective analysis of medical records were performed for 61 eyes (32 patients) diagnosed with macular telangiectasia type 2. The visual acuity at diagnosis was compared with that at the final visit. In addition, cases were classified into three grades based on optical coherence tomography (OCT) findings: grade 1, inner retinal cavities only; grade 2, outer retinal cavities with ellipsoid zone disruption; and grade 3, ellipsoid zone disruption with proliferation of retinal pigment epithelium. Change in the grade during the follow-up was verified. In addition, visual acuities were compared between eyes with and without a change in grade.Results: The mean follow-up period was 41.5 ± 33.2 months. Visual acuity had deteriorated significantly from the mean logarithm of the minimal angle of resolution 0.23 ± 0.26 at diagnosis to a mean of 0.31 ± 0.31 at the final visit (p < 0.001). When classified using OCT, 65.6%, 22.9%, and 11.5% were grades 1, 2, and 3, respectively, at diagnosis and 47.5%, 36.1%, and 16.4% at the final visit. Progression of grade was noted in 22.9%. A higher degree of visual deterioration was noted in eyes showing progression than in eyes without (p = 0.002).Conclusions: During the long-term follow-up period, visual deterioration was noted in patients with macular telangiectasia type 2. However, the degree of deterioration was not high. Progression in the disruption of the retinal microstructure was the likely cause of visual deterioration.
Clinical Factors Affecting Recovery Periods of Vascular and Idiopathic Acquired Paralytic Strabismus
Authors: Yoon Su-Min , Ha Suk-Gyu , Seo Yeong-Woo , Kim Seung-Hyun
Published: August 2021

Purpose: Clinical factors affecting the recovery period in patients with vascular or idiopathic paralytic strabismus were evaluated.Methods: This study involved a retrospective review of medical records of patients diagnosed with vascular and idiopathic acquired paralytic strabismus. Vascular paralysis was defined in cases of hypertension, diabetes mellitus, or cardiovascular disease. The angle of deviation and limitation of extraocular movement were evaluated at each visit. Recovery was defined as the absence of diplopia and complete resolution of limitation of extraocular movement. Factors affecting recovery success and recovery period were analyzed.Results: We retrospectively reviewed data of 145 patients consisting of 87 with vascular paralytic strabismus (cranial nerve [CN] III: 21, CN IV: 28, CN VI: 38) and 58 with idiopathic paralytic strabismus (CN IV: 20, CN VI: 24, CN III: 14). The recovery rate did not significantly differ between vascular (60.9%) and idiopathic (63.8%) groups (p = 0.15). The recovery period was longer in the vascular group (130.1 ± 145.1 days) than in the idiopathic group (92.6 ± 76.6) (p = 0.02). Age at onset was significantly associated with the recovery period in both vascular and idiopathic groups. In the vascular group, the recovery periods were 107.4 ± 74.8 days in CN III palsy, 97.2 ± 51.9 days in CN IV palsy, and 159.3 ± 194.1 days in CN VI palsy. The recovery period was significantly longer in patients with CN VI palsy (p = 0.03). Hypertension was significantly influencing the recovery period in patients with vascular CN VI palsy (odds ratio = 2.54, p = 0.01).Conclusions: The recovery period was longer in patients with vascular paralytic strabismus than in patients with idiopathic paralytic strabismus. Recovery rates were not significantly different between groups. In patients with vascular CN VI palsy, a history of hypertension was significantly associated with the recovery period.
First report of a disease caused by Bacillus cereus in cultured loach Paramisgurnus dabryanus
Authors: Luo Z , Sun H , Hao S , Ma Y , Zhang Z , Feng S , Bai X
Published: August 2021

Bacillus cereus is commonly considered a bacterium pathogenic to mammals, but several studies have suggested that it also induces diseases in fish. In 2017 and 2018, 2 strains of B. cereus, NQ-2017-17 and NQ-2018-8, were isolated from diseased large-scale loach Paramisgurnus dabryanus in Tianjin, China, and were considered to be the pathogens responsible for the disease. These stains were identified as B. cereus based on the results of 16S rDNA gene sequence analysis, Vitek biochemical tests, physiological and biochemical tests, and B. cereus group species-specific PCR. Strains NQ-2017-7 and NQ-2018-8 were found to contain virulence genes (e.g. hblA, hblC, hblD, entFM, and bceT) causing pathological damage to the spleen, kidneys, liver, and gills of loach. The median lethal dose (LD50) of NQ-2017-7 and NQ-2018-8 for loach were 1.0 ×106.64 and 1.0 ×106.49 CFU ml-1, respectively. To our knowledge, this is the first report of loach disease caused by a member of the genus Bacillus.
Orthogonal polarization spectral imaging
Authors: Černý V , Turek Z , Pařízková R
Published: August 2021

The microcirculation plays a crucial role in the interaction between blood and tissues both in physiological and pathophysiological states. Despite its critical role in numerous diseases including diabetes, hypertension, sepsis or multiple organ failure, methods for direct visualization and quantitative assessment of human microcirculation at the bedside are limited. Orthogonal polarization spectral (OPS) imaging is a relatively new noninvasive method for assessment of human microcirculation without using fluorescent dyes. Recent clinical studies using OPS imaging in various pathological states have shown a wide spectrum of different clinical applications with evident impact on the diagnosis, treatment or prognosis assessment. Thus, there is a great effort to validate OPS imaging for various clinical purposes. The principles of OPS imaging, validation studies, its advantages, limitations, methods of quantitative assessment and current experience in clinical practice are discussed.
Fluorescent advanced glycation end products in the detection of factual stages of cartilage degeneration
Authors: Handl M , Filová E , Kubala M , Lánský Z , Koláčná L , Vorlíček J , Trč T , Amler E
Published: August 2021

Patients treated for knee disorders were included in this study. They were examined clinically (Lequesne and Tegner scores) and by standard X-ray investigation. Patients underwent a surgical procedure, either arthroscopy or knee replacement. At the initial phase of surgery, a sample of cartilage was taken for laboratory examination. Progression of the disorder and the clinical examination was correlated with the actual state of the cartilage using a novel fluorescence approach. The intrinsic fluorescence of cartilages was shown as a suitable and sensitive method for detection of the actual state of cartilages because the correlation with X-ray examination and clinical status was found. Intrinsic fluorescence properties of cartilages from patients with chondropathy and osteoarthritis were described and found to be age-dependent. We also observed a higher concentration of advanced glycation end products due to inflammatory and/or degenerative processes in the cartilage. In addition, acute pathological changes due to diseases such as meniscal lesions or anterior cruciate ligament rupture caused a significant increase of formation of advanced glycation end products even in the group of young patients. In fact, such an observation could be crucial and important for the detection of knee conditions suspected of early meniscal and/or ACL lesions especially among young patients.
Evaluation of ECG time intervals in a rabbit model of anthracycline-induced cardiomyopathy: a useful tool for assessment of cardioprotective agents
Authors: Potáčová A , Adamcová M , Čajnáková H , Hrbatová L , Štěrba M , Popelová O , Šimůnek T , Poňka P , Geršl V
Published: August 2021

The aim of this study was to analyze the ECG time intervals in the course of the development of chronic anthracycline cardiomyopathy in rabbits. Furthermore, this approach was employed to study the effects of a model cardioprotective drug (dexrazoxane) and two novel iron chelating compounds--salicylaldehyde isonicotinoyl hydrazone (SIH) and pyridoxal 2-chlorobenzoyl hydrazone (o-108). Repeated daunorubicin administration induced a significant and progressive prolongation of the QRS complex commencing with the eighth week of administration. At the end of the study, we identified a significant correlation between QRS duration and the contractility index dP/dt(max) (r = -0.81; P<0.001) as well as with the plasma concentrations of cardiac troponin T (r = 0.78; P<0.001). In contrast, no alterations in ECG time intervals were revealed in the groups co-treated with either dexrazoxane or both novel cardioprotective drugs (SIH, o-108). Hence, in this study, the QRS duration is for the first time shown as a parameter suitable for the non-invasive evaluation of the anthracycline cardiotoxicity and cardioprotective effects of both well established and investigated drugs. Moreover, our results strongly suggest that novel iron chelators (SIH and o-108) merit further study as promising cardioprotective drugs against anthracycline cardiotoxicity.
SEKOLAH DARING DAN KETERGANTUNGAN TELEPON GENGGAM PADA REMAJA
Authors: Nurwulan Nurul Retno
Published: August 2021

Adolescents engage in smartphones cognitively and emotionally. More evidence suggests that they tend to be dependent on and addicted to smartphones. However, smartphone usage is inevitable during the COVID-19 pandemic since students need to attend online class. Previous studies have developed measurement method to evaluate smartphone addiction. This study evaluated 13 to 15-year-old adolescents’ self-awareness of smartphone addiction using problematic use of mobile phones (PUMP) approach. Group discussions were conducted with adolescents who did self-assessment using the problematic use of mobile phones scale. The main findings of group discussions include drivers of excessive smartphone use, smartphone usage behavior when they are with family or friends, barriers to healthier smartphone use, and nighttime habits. Despite its advantages during the COVID-19 pandemic, parents need to supervise and to encourage their children to use smartphones wisely.
Myocardial Scar Characterization and Future Ventricular Arrhythmia in Patients With Ischemic Cardiomyopathy and an Implantable Cardioverter-Defibrillator
Authors: Noordman Alwin B. P. , Maass Alexander H. , Groenveld Hessel , Mulder Bart A. , Rienstra Michiel , Blaauw Yuri
Published: August 2021

Background: Implantable cardioverter-defibrillator (ICD) therapy is associated with several deleterious effects, which can be reduced by antiarrhythmic drugs or catheter ablation. However, it is largely unknown which patients might benefit from these therapies. Therefore, this study aimed to investigate whether myocardial scar characterization improves risk stratification for ventricular arrhythmia (VA) occurrence in patients with ischemic cardiomyopathy and an ICD.

Methods: In this study, 82 patients with ischemic cardiomyopathy who received an ICD were enrolled retrospectively. Late gadolinium enhancement cardiac magnetic resonance (LGE-CMR) images were analyzed using an investigational software tool to obtain quantitative data regarding the total scar, core, and border zone (BZ). Data regarding the QRS complex was obtained from electrocardiography (ECG). The primary endpoint was appropriate ICD therapy.

Results: During a median follow-up duration of 3.98 years [interquartile range (IQR) 2.89–5.14 years], appropriate therapy occurred in 24 (29.3%) patients. Patients with appropriate ICD therapy had a significantly larger total scar mass [60.0 (IQR 41.2–73.4) vs. 43.3 (IQR 31.2–61.2) g; P = 0.009] and BZ mass [32.9 (IQR 26.9–42.4) vs. 24.5 (IQR 18.8–32.5) g; P = 0.001] than those without appropriate therapy. In multivariable Cox regression analyses, total scar mass [hazard ratio (HR) 1.02 [95% confidence interval (CI) 1.00–1.04]; P = 0.014] and BZ mass (HR 1.04 [95% CI 1.01–1.07]; P = 0.009) independently predicted appropriate ICD therapy. Core mass and the QRS complex, however, were not significantly associated with the primary endpoint.

Conclusion: LGE-CMR-based, but not ECG-based myocardial scar characterization improves risk stratification for VA occurrence in patients with ischemic cardiomyopathy who received an ICD.
School Leaders' Perspectives on Successful Leadership: A Mixed Methods Case Study of a Private School Network in Pakistan
Authors: Raza Mehwish , Gilani Nadia , Waheed Syed Abdul
Published: August 2021

Private school culture dominates the public-school culture in Pakistan. With no central regulating organization, private schools in the country autonomously construct their educational philosophy that underpins curriculum choice, pedagogic approaches, and school operations. In this perspective, there is an increasing inquisitiveness in the understanding of what determines a private school as a “successful” school. The researchers intend to understand the determinants of a successful private school and aim to explore the leadership behaviors of head teachers of such schools in Pakistan. The Beaconhouse School System (BSS), the largest private school system in Pakistan, took part in this case study. A sample of a total of 128 participants, comprising of teachers (n = 120), School Group Heads (SGH) (n = 4) and school head teachers (n = 4) of four most successful primary schools of BSS, was drawn to participate in this case study employing a mixed-methods design. Two survey instruments, Determinants of School Success (DSS) and Leadership Practice Index (LPI) were developed on a five-point Likert Scale and applied to identify four most successful primary schools of BSS. It was found that head teachers had established a whole-school approach towards students high achievement, promoted a culture of trust, commitment, shared vision, practiced distributed leadership and involved all stakeholders in creating a shared sense of direction for the school. Recommendations have been generated for improving the performance of school leaders.
Measuring Teacher Buy-in for the Texas Pay-for-Performance Program
Authors: Lee Jaehoon , Strong Michael , Hamman Doug , Zeng Yifang
Published: August 2021

Teacher buy-in is a critical component for the success of any educational reform, especially one involving evaluation and compensation. We report on an instrument developed to measure teacher buy-in for district-developed designation plans associated with a state pay-for-performance (PFP) program, and teacher responses. We used modern test theory to investigate the instrument’s psychometric properties, a procedure often missing from research reports of self-designed surveys. A sample of 3,001 elementary, middle school, and high school teachers in Texas school districts participated in the survey. Our results suggest satisfactory reliability of the instrument and adequate discriminant validity in measuring distinct but related aspects of teacher buy-in. In addition, we found that teacher support for PFP as instantiated in their particular districts was generally high, but still buy-in levels varied significantly among different teacher groupings, pointing the way for future developers of pay-for-performance schemes to improve or maximize their acceptance.
Estrogen as an Essential Resource and the Coexistence of ER+ and ER– Cancer Cells
Authors: Kareva Irina , Brown Joel S.
Published: August 2021

Diagnosis of estrogen sensitivity in breast cancer is largely predicated on the ratio of ER+and ER–cancer cells obtained from biopsies. Estrogen is a growth factor necessary for cell survival and division. It can also be thought of as an essential resource that can act in association with other nutrients, glucose, glutamine, fatty acids, amino acids, etc. All of these nutrients, collectively or individually, may limit the growth of the cancer cells (Liebig’s Law of the Minimum). Here we model estrogen susceptibility in breast cancer as a consumer-resource interaction: ER+cells require both estrogen and glucose as essential resources, whereas ER–only require the general resource. The model predicts that when estrogen is the limiting factor, other nutrients may go unconsumed and available at higher levels, thus permitting the invasion of ER–cells. Conversely, when ER–cells are less efficient on glucose than ER+cells, then ER–cells limited by glucose may be susceptible to invasion by ER+cells, provided that sufficient levels of estrogen are available. ER+cells will outcompete ER–cells when estrogen is abundant, resulting in low concentrations of interstitial glucose within the tumor. In the absence of estrogen, ER–cells will outcompete ER+cells, leaving a higher concentration of interstitial glucose. At intermediate delivery rates of estrogen and glucose, ER+and ER–cells are predicted to coexist. In modeling the dynamics of cells in the same tumor with different resource requirements, we can apply concepts and terms familiar to many ecologists. These include: resource supply points,R∗, ZNGI (zero net growth isoclines), resource depletion, and resource uptake rates. Based on the circumstances favoring ER+vs. ER–breast cancer, we use the model to explore the consequences of therapeutic regimens that may include hormonal therapies, possible roles of diet in changing cancer cell composition, and potential for evolutionarily informed therapies. More generally, the model invites the viewpoint that cancer’s eco-evolutionary dynamics are a consumer-resource interaction, and that other growth factors such as EGFR or androgens may be best viewed as essential resources within these dynamics.
Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy
Authors: Atkins Andrew , Chung Cheng-Han , Allen Alexander G. , Dampier Will , Gurrola Theodore E. , Sariyer Ilker K. , Nonnemacher Michael R. , Wigdahl Brian
Published: August 2021

As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
The Role of Mitochondrial DNA Variation in Drug Response: A Systematic Review
Authors: Jones Samantha W. , Ball Amy L. , Chadwick Amy E. , Alfirevic Ana
Published: August 2021

Background: The triad of drug efficacy, toxicity and resistance underpins the risk-benefit balance of all therapeutics. The application of pharmacogenomics has the potential to improve the risk-benefit balance of a given therapeutic via the stratification of patient populations based on DNA variants. A growth in the understanding of the particulars of the mitochondrial genome, alongside the availability of techniques for its interrogation has resulted in a growing body of literature examining the impact of mitochondrial DNA (mtDNA) variation upon drug response.

Objective: To critically evaluate and summarize the available literature, across a defined period, in a systematic fashion in order to map out the current landscape of the subject area and identify how the field may continue to advance.

Methods: A systematic review of the literature published between January 2009 and December 2020 was conducted using the PubMed database with the following key inclusion criteria: reference to specific mtDNA polymorphisms or haplogroups, a core objective to examine associations between mtDNA variants and drug response, and research performed using human subjects or human in vitro models.

Results: Review of the literature identified 24 articles reporting an investigation of the association between mtDNA variant(s) and drug efficacy, toxicity or resistance that met the key inclusion criteria. This included 10 articles examining mtDNA variations associated with antiretroviral therapy response, 4 articles examining mtDNA variants associated with anticancer agent response and 4 articles examining mtDNA variants associated with antimicrobial agent response. The remaining articles covered a wide breadth of medications and were therefore grouped together and referred to as “other.”

Conclusions: Investigation of the impact of mtDNA variation upon drug response has been sporadic to-date. Collective assessment of the associations identified in the articles was inconclusive due to heterogeneous methods and outcomes, limited racial/ethnic groups, lack of replication and inadequate statistical power. There remains a high degree of idiosyncrasy in drug response and this area has the potential to explain variation in drug response in a clinical setting, therefore further research is likely to be of clinical benefit.
NEDD8 Deamidation Inhibits Cullin RING Ligase Dynamics
Authors: Mohanty Priyesh , Chatterjee Kiran Sankar , Das Ranabir
Published: August 2021

Cullin-RING ligases (CRLs) are a significant subset of Ubiquitin E3 ligases that regulate multiple cellular substrates involved in innate immunity, cytoskeleton modeling, and cell cycle. The glutamine deamidase Cycle inhibitory factor (Cif) from enteric bacteria inactivates CRLs to modulate these processes in the host cell. The covalent attachment of a Ubiquitin-like protein NEDD8 catalytically activates CRLs by driving conformational changes in the Cullin C-terminal domain (CTD). NEDDylation results in a shift from a compact to an open CTD conformation through non-covalent interactions between NEDD8 and the WHB subdomain of CTD, eliminating the latter’s inhibitory interactions with the RING E3 ligase-Rbx1/2. It is unknown whether the non-covalent interactions are sufficient to stabilize Cullin CTD’s catalytic conformation. We studied the dynamics of Cullin-CTD in the presence and absence of NEDD8 using atomistic molecular dynamics (MD) simulations. We uncovered that NEDD8 engages in non-covalent interactions with 4HB/αβ subdomains in Cullin-CTD to promote open conformations. Cif deamidates glutamine 40 in NEDD8 to inhibit the conformational change in CRLs by an unknown mechanism. We investigated the effect of glutamine deamidation on NEDD8 and its interaction with the WHB subdomain post-NEDDylation using MD simulations and NMR spectroscopy. Our results suggest that deamidation creates a new intramolecular salt bridge in NEDD8 to destabilize the NEDD8/WHB complex and reduce CRL activity.
Stochastic Model of the Adaptive Immune Response Predicts Disease Severity and Captures Enhanced Cross-Reactivity in Natural Dengue Infections
Authors: Nguyen Hung D. , Chaudhury Sidhartha , Waickman Adam T. , Friberg Heather , Currier Jeffrey R. , Wallqvist Anders
Published: August 2021

The dengue virus circulates as four distinct serotypes, where a single serotype infection is typically asymptomatic and leads to acquired immunity against that serotype. However, the developed immunity to one serotype is thought to underlie the severe manifestation of the disease observed in subsequent infections from a different serotype. We developed a stochastic model of the adaptive immune response to dengue infections. We first delineated the mechanisms initiating and sustaining adaptive immune responses during primary infections. We then contrasted these immune responses during secondary infections of either a homotypic or heterotypic serotype to understand the role of pre-existing and reactivated immune pathways on disease severity. Comparison of non-symptomatic and severe cases from heterotypic infections demonstrated that overproduction of specific antibodies during primary infection induces an enhanced population of cross-reactive antibodies during secondary infection, ultimately leading to severe disease manifestations. In addition, the level of disease severity was found to correlate with immune response kinetics, which was dependent on beginning lymphocyte levels. Our results detail the contribution of specific lymphocytes and antibodies to immunity and memory recall that lead to either protective or pathological outcomes, allowing for the understanding and determination of mechanisms of protective immunity.
Precision N-Glycoproteomic Profiling of Murine Peritoneal Macrophages After Different Stimulations
Authors: Yang Lujie , Gong Tianqi , Shen Huali , Pei Jiangnan , Zhang Lei , Zhang Quanqing , Huang Yuanyu , Hu Zuojian , Pan Ziyue , Yang Pengyuan , Lin Ling , Yu Hongxiu
Published: August 2021

Macrophages are important immune cells that participate in both innate and adaptive immune responses, such as phagocytosis, recognition of molecular patterns, and activation of the immune response. In this study, murine peritoneal macrophages were isolated and then activated by LPS, HSV and VSV. Integrative proteomic and precision N-glycoproteomic profiling were conducted to assess the underlying macrophage activation. We identified a total of 587 glycoproteins, including 1239 glycopeptides, 526 monosaccharide components, and 8326 intact glycopeptides in glycoproteomics, as well as a total of 4496 proteins identified in proteomic analysis. These glycoproteins are widely involved in important biological processes, such as antigen presentation, cytokine production and glycosylation progression. Under the stimulation of the different pathogens, glycoproteins showed a dramatic change. We found that receptors in the Toll-like receptor pathway, such as Tlr2 and CD14, were increased under LPS and HSV stimulation. Glycosylation of those proteins was proven to influence their subcellular locations.
Activated γδ T Cells With Higher CD107a Expression and Inflammatory Potential During Early Pregnancy in Patients With Recurrent Spontaneous Abortion
Authors: Yu Long , Zhang Yang , Xiong Jinfeng , Liu Jianjun , Zha Ying , Kang Qi , Zhi Pan , Wang Qiang , Wang Hui , Zeng Wanjiang , Huang Yafei
Published: August 2021

Previous studies have reported the involvement of γδ T cells in recurrent spontaneous abortion (RSA); however, both pathogenic and protective effects were suggested. To interrogate the role of γδ T cells in RSA, peripheral blood from RSA patients and healthy women with or without pregnancy were analyzed for γδ T cells by flow cytometry (n= 9–11 for each group). Moreover, the decidua from pregnant RSA patients and healthy controls (RSA-P and HC-P group, respectively) was simultaneously stained for γδ T cells by immunohistochemistry (IHC) and bulk sequenced for gene expression. Our results demonstrated that the frequencies of peripheral γδ T cells and their subpopulations in RSA patients were comparable to that in healthy subjects, but the PD1 expression on Vδ2+cells was increased in pregnant patients. Furthermore, peripheral Vδ2+cells in RSA-P patients demonstrated significantly increased expression of CD107a, as compared to that in pregnant healthy controls. In addition, RSA-P patients had higher proportion of IL-17A-secreting but not IL-4-secreting Vδ2+cells compared to the control groups. In decidua, an inflammatory microenvironment was also evident in RSA-P patients, in whichCCL8expression and the infiltration of certain immune cells were higher than that in the HC-P group, as revealed by transcriptional analysis. Finally, although the presence of γδ T cells in decidua could be detected during pregnancy in both RSA patients and healthy subjects by multicolor IHC analysis, the expression of CD107a on γδ T cells was markedly higher in the RSA-P group. Collectively, our results indicated that the increased activation, cytotoxicity, and inflammatory potential of peripheral and/or local γδ T cells might be responsible for the pathogenesis of RSA. These findings could provide a better understanding of the role of γδ T cells in RSA and shed light on novel treatment strategies by targeting γδ T cells for RSA patients.
PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage
Authors: Nilsson Jonas Birkelund , Grifoni Alba , Tarke Alison , Sette Alessandro , Nielsen Morten
Published: August 2021

The use of minimal peptide sets offers an appealing alternative for design of vaccines and T cell diagnostics compared to conventional whole protein approaches. T cell immunogenicity towards peptides is contingent on binding to human leukocyte antigen (HLA) molecules of the given individual. HLA is highly polymorphic, and each variant typically presents a different repertoire of peptides. This polymorphism combined with pathogen diversity challenges the rational selection of peptide sets with broad immunogenic potential and population coverage. Here we propose PopCover-2.0, a simple yet highly effective method, for resolving this challenge. The method takes as input a set of (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and pathogen strain annotation together with information on HLA allele frequencies, and identifies peptide sets with optimal pathogen and HLA (class I and II) coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was confirmed by experimentally validating the peptide pools for T cell responses in a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an effective method for rational selection of peptide subsets with broad HLA and pathogen coverage. The tool is available at https://services.healthtech.dtu.dk/service.php?PopCover-2.0.
Probing Electronic Properties of CVD Monolayer Hexagonal Boron Nitride by an Atomic Force Microscope
Authors: Deng Shiyu , Gu Yanyun , Wan Xi , Gao Mingliang , Xu Shijia , Chen Kun , Chen Huanjun
Published: August 2021

Ultrathin hexagonal boron nitride (h-BN) has recently attracted a lot of attention due to its excellent properties. With the rapid development of chemical vapor deposition (CVD) technology to synthesize wafer-scale single-crystal h-BN, the properties of h-BN have been widely investigated with a variety of material characterization techniques. However, the electronic properties of monolayer h-BN have rarely been quantitatively determined due to its atomically thin thickness and high sensitivity to the surrounding environment. In this work, by the combined use of AFM (atomic force microscope) PeakForce Tunneling (PF-TUNA) mode and Kevin probe force microscopy (KPFM) model, both the electrical resistivity (529 MΩ cm) and the inherent Fermi level (∼4.95 eV) of the as-grown monolayer h-BN flakes on the copper substrate have been quantitatively analyzed. Moreover, direct visualization of the high-temperature oxidation-resistance effect of h-BN nanoflakes has been presented. Our work demonstrates a direct estimation of the electronic properties for 2D materials on the initial growth substrate without transfer, avoiding any unwanted contaminations introduced during the transfer process. The quantitative analysis by state-of-the-art atomic force microscope techniques implies that monolayer h-BN can be employed as an atomically thin and high-quality insulator for 2D electronics, as well as a high-temperature antioxidation layer for electronic device applications.
Elevated Pancreatic Enzymes in ICU Patients With COVID-19 in Wuhan, China: A Retrospective Study
Authors: Ding Peili , Song Bin , Liu Xuelin , Fang Xing , Cai Hongliu , Zhang Dingyu , Zheng Xia
Published: August 2021

Background: Pancreatic enzyme elevation has been reported in patients with COVID-19 during the pandemic. However, with the shortage of medical resources and information, several challenges are faced in the examination and treatment of this condition in COVID-19 patients. There is little information on whether such condition is caused by pancreatic injury, and if this is a warning sign of life threatening complications like multiple organ failure in patients. The objective of this study is to explore the relationship between elevated pancreatic enzymes and the underlying risk factors during the management of COVID-19 patients.

Method: A total of 55 COVID-19 patients admitted to the intensive care unit (ICU) of Wuhan Jinyintan hospital from January 1 to March 30, 2020 were enrolled in this study. All participants underwent transabdominal ultrasound imaging to assess their pancreas.

Results: Out of the 55 patients, three patients had pancreatitis, 29 (52.7%) with elevated pancreatic enzymes, and 23 (41.8%) without. The most common symptoms of patients with COVID-19 were fever and cough. There was no statistical difference in most baseline characteristics except myalgia on admission. Compared with those having normal enzyme levels, patients with elevated pancreatic enzymes had higher rates of mortality (79.3 vs. 52.2%; P = 0.038), and lower rates of discharge (20.7 vs. 47.8%; P = 0.038). Patients with elevated enzymes had higher incidence of mechanical ventilation (P = 0.004) and kidney injury (P = 0.042) than patients without elevated pancreatic enzymes. The results of multivariable logistic analysis showed that the odds ratio were 10.202 (P = 0.002) for mechanical ventilation and 7.673 (P = 0.014) for kidney injury with the elevated enzymes vs. the normal conditions.

Conclusions: The findings show that the incidences of pancreatic enzymes elevation are not low in critical COVID-19 patients and only a few of them progressed to acute pancreatitis (AP). Increased pancreatic enzymes levels is associated with poor prognosis in COVID-19 patients. In addition, the kidney injury and oxygenation degradation are associated with the pancreatic enzymes elevation in COVID-19 patients.
Simultaneous Multiplex Genome Engineering via Accelerated Natural Transformation in Bacillus subtilis
Authors: Deng Aihua , Sun Zhaopeng , Wang Tiantian , Cui Di , Li Lai , Liu Shuwen , Huang Fei , Wen Tingyi
Published: August 2021

Multiplex engineering at the scale of whole genomes has become increasingly important for synthetic biology and biotechnology applications. Although several methods have been reported for engineering microbe genomes, their use is limited by their complex procedures using multi-cycle transformations. Natural transformation, involving in species evolution by horizontal gene transfer in many organisms, indicates its potential as a genetic tool. Here, we aimed to develop simultaneous multiplex genome engineering (SMGE) for the simple, rapid, and efficient design of bacterial genomes via one-step of natural transformation in Bacillus subtilis. The transformed DNA, competency factors, and recombinases were adapted to improved co-editing frequencies above 27-fold. Single to octuplet variants with genetic diversity were simultaneously generated using all-in-one vectors harboring multi-gene cassettes. To demonstrate its potential application, the tyrosine biosynthesis pathway was further optimized for producing commercially important resveratrol by high-throughput screening of variant pool in B. subtilis. SMGE represents an accelerated evolution platform that generates diverse multiplex mutations for large-scale genetic engineering and synthetic biology in B. subtilis.
DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data
Authors: Loos Daniel , Zhang Lu , Beemelmanns Christine , Kurzai Oliver , Panagiotou Gianni
Published: August 2021

Trillions of microbes representing all kingdoms of life are resident in, and on, humans holding essential roles for the host development and physiology. The last decade over a dozen online tools and servers, accessible via public domain, have been developed for the analysis of bacterial sequences; however, the analysis of fungi is still in its infancy. Here, we present a web server dedicated to the comprehensive analysis of the human mycobiome for (i) translating raw sequencing reads to data tables and high-standard figures, (ii) integrating statistical analysis and machine learning with a manually curated relational database and (iii) comparing the user’s uploaded datasets with publicly available from the Sequence Read Archive. Using 1,266 publicly available Internal transcribed spacers (ITS) samples, we demonstrated the utility of DAnIEL web server on large scale datasets and show the differences in fungal communities between human skin and soil sites.