bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS in tetraploid potato: Identification and validation of SNP markers associated with glycoalkaloid content
Authors: Vos Peter G. , Paulo M. João , Bourke Peter M. , Maliepaard Chris A. , Eeuwijk Fred A. van , Visser Richard G.F , Eck Herman J. van 
Published: August 2022

AbstractGenome wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in tubers. SGAs are secondary metabolites in theSolanaceaefamily, functional as a defence against various pests and pathogens and in high quantities toxic for humans. With GWAS we identified five quantitative trait loci (QTL) of whichSga1.1, Sgr8.1andSga11.1were validated, but notSga3.1andSgr7.1. In the bi-parental populationsSga5.1andSga7.1were mapped, but these were not identified with GWAS. The QTLsSga1.1, Sga7.1, Sgr7.1, Sgr8.1co-localize with genesGAME9, GAME 6 / GAME 11, SGT1 and SGT2, respectively. For other genes involved in SGA synthesis no QTLs were identified. The results of this study illustrate a number of pitfalls in GWAS of which population structure seems the most important. We also show that introgression breeding for disease resistance has introduced new haplotypes to the gene pool involved in higher SGA levels in certain pedigrees. Finally we show that high SGA levels remain unpredictable in potato but that α-solanine / α-chaconine ratio has a predictable outcome with specificSGT1andSGT2haplotypes.
A normalized model based on Taqman real-time PCR assay for quantitative comparison of chicken adulteration in raw and heat-treated hamburgers
Authors: Sarlak Zahra , Rezvani Nayebali , Rouhi Milad , Shojaee-Aliabadi Saeedeh , Hosseini Hedayat 
Published: August 2022

Abstract
Mislabeling of hamburgers with undeclared chicken has frequently been reported. A fast TaqMan real-time PCR assay was developed to estimate chicken percentage in raw and heat-treated hamburgers in the current work. The calibration curve was plotted with the normalization approach (ΔCt; the difference calculation between chicken-cytb and eukaryotic-18S rRNA assays) for five reference chicken mixtures (100-0.01%) using a duplex TaqMan-qPCR protocol. The R2 and efficiency values of the normalized curve were 0.9993 and ~100%, respectively. In the validation plan, analysis of model samples (raw, oven-cooked and autoclaved) under repeatability conditions represented the bias values within the range of ±25% and RSD values <25%, except for a few autoclaved model samples. Therefore, this developed and validated model could be considered a useful and reliable method for estimating chicken species (with a sensitivity of 0.01%) in raw and cooked hamburgers.
Nanophotonic Reservoir Computing for COVID-19 Pandemic Forecasting
Authors: Liu Bocheng , Xie Yiyuan , Liu Weichen , Jiang Xiao , Ye Yichen , Song Tingting , Chai Junxiong , Feng Manying , Yuan Haodong 
Published: August 2022

Abstract
The coronavirus disease 2019 (COVID-19) has spread worldwide in unprecedented speed, and diverse negative impacts have seriously endangered human society. Accurately forecasting the number of COVID-19 cases can help governments and public health organizations develop the right prevention strategies in advance to contain outbreaks. In this work, a long-term six-month COVID-19 pandemic forecast in second half of 2021 and a short-term 30-day daily ahead COVID-19 forecast in December 2021 are successfully implemented via a novel nanophotonic reservoir computing (RC) based on silicon optomechanical oscillators (OMO) with photonic crystal (PhC) cavities, where these nonlinear time series related to COVID-19 are mapped to the high-dimensional nonlinear space via the optical nonlinear properties of nanophotonic reservoir computing. The testing-dataset forecast results of new cases, new deaths, cumulative cases, and cumulative deaths for six countries demonstrate that the forecasted blue curves are awfully close to the real red curves with exceedingly small forecast errors. Moreover, the forecast results commendably reflect the variations of the actual case data, revealing the different epidemic transmission laws in developed and developing countries. More importantly, the daily ahead forecast results during December 2021 of four kinds of cases for six countries illustrate that the daily forecasted values are highly coincident with the real values, while the relevant forecast errors are tiny enough to verify the good forecasting competence of COVID-19 pandemic dominanted by Omicron strain. Therefore, the implemented nanophotonic reservoir computing can provide some foreknowledge on prevention strategy and healthcare management for COVID-19 pandemic.
Comparison between Sofosbuvir free regimen and Sofosbuvir based regimens in the treatment of chronic HCV patients with chronic renal failure
Authors: ramadan ahmed ali , Amer Ahmed Aymen , Elakel Wafaa , Fouad Ahmed 
Published: August 2022

Abstract
Background: HCV infection is a major burden in Egypt as it affects 15% of the population. The treatment depends upon direct acting antivirals(DAAs). It was implied earlier that Sofosbuvir(SOF) better be avoided for potential toxic effects in patients with moderate to severe renal impairment. This study aims to evaluate the efficacy and safety of SOF-based regimens against SOF-free in this special population of patients Methods: This is a retrospective study where data for all HCV patients with chronic kidney disease including those with end stage renal disease and on haemodialysis were reviewed and 6607 patients were enrolled according to the National Committee for Control of Viral Hepatitis (NCCVH) in Egypt; these patients received variety of DAAs regimens including SOF-based and SOF-free regimens, and were categorized into two groups based on renal profile.Results: Sustained virological response (SVR) rate in this study was of 98.3%; 98.7% for those who were on SOF-based regimen and 95.6% for those administered SOF-free regimen. Regarding patients who were on haemodialysis, SVR rate was 100% in patients who received SOF-based regimen opposite to SVR rate of 91.2% in those who received SOF-free regimen. Moreover, in patients with moderate renal affection ‘grade 3 CKD’ SVR rates were 98.7% with SOF-based regimens and 97.6% for SOF-free regimens. Conclusion: SOF-based regimens at full dose are considered more effective than SOF-free regimens in patients with moderate to severe renal impairment with good safety profile and better SVR rate.
Impulsivity and depression in Chinese male methamphetamine abusers during chronic withdrawal: the mediating role of fatigue
Authors: Tong Siyu , Zhou Siyao , Sun Shiyu , Hong Lan , Wang Chaoyue , Peng Chenhui , Jing Wei , Jiang Yile , He He , Zhao Ke 
Published: August 2022

Abstract
Background: Impulsivity and depression are considered to have a crucial role in the process of Methamphetamine dependence withdrawal. However, little is known about the underlying factors that influence the relationship in Methamphetamine users. Previous studies indicated that fatigue was present in a variety of neurological diseases and tended to increase during late Methamphetamine withdrawal. Thus, this study aimed to explore whether fatigue takes part in mediating the association between impulsivity and depression. Methods: 112 Methamphetamine users in late withdrawal period were recruited from Wenzhou Huanglong Detoxification Institute of Zhejiang province. The conditions of impulsivity, fatigue and depression were respectively measured by Barratt Impulsiveness Scale (BIS-11), the 14-item Fatigue Scale (FS-14) and the 9-item Patient Health Questionnaire (PHQ-9). Results: Our finding suggested that impulsivity positively correlated with fatigue and depression. Mediating effect analysis showed that fatigue has a mediating role in the relationship between impulsivity and depression. Conclusion: Results confirm and extend the research on the mechanisms of impulsivity and depression as well as fatigue of METH users during late methamphetamine withdrawal. These findings suggest that interventions designed to reduce depression may also be effective if they focus on cut down on feelings of fatigue in METH users, particularly for METH users with higher levels of impulsivity.
Perception of risk of hypertension related complications and adherence to antihypertensive drugs: a primary healthcare based cross-sectional study
Authors: Shiraly Ramin , Jeihooni Ali Khani , Shirazi Rozita Bakhshizadeh 
Published: August 2022

Abstract
Background
Treatment of hypertension often requires lifelong drug therapy; blood pressure control is suboptimal in more than half of treated hypertensive patients. Few studies have focused on perceived risk of hypertension sequelae as a determinant of adherence to antihypertensive medications.
Methods
We assessed 600 hypertensive patients aged 31 to 85 years being served by primary healthcare centers in Shiraz, Iran. The outcome of interest was adherence to antihypertensive medications measured by the 8-item Morisky Medication Adherence Scale (MMAS-8). In addition to demographic information, participants were asked about duration of antihypertensive therapy, number of drugs taken concurrently and their perceived risk of complications of high blood pressure. Multivariate logistic regression analysis was used to identify independent factors associated with better drug adherence.
Results
Nearly half (48.8%) of participants had uncontrolled hypertension. Just over one fifth (22.3%) of all the patients reported high adherence to antihypertensive medications. Independent factors associated with better adherence to antihypertensive medications were higher educational level (OR: 1.71, CI 95%: 1.06–2.75), being a never smoker (OR: 1.62, CI 95%: 1.06–2.46), having easy access to healthcare services (OR: 1.91, CI 95%: 1.10–3.35), lower mean treatment duration (OR: 0.96, CI 95%: 0.92–0.99), and having higher perceived risk of hypertension-related complications (OR:2.34, CI 95%: 1.52–3.60).
Conclusion
High perceived risk of hypertension-related complications is significantly associated with adherence to antihypertensive therapy. Our findings suggest that primary care physicians should regularly emphasize on negative consequences of uncontrolled/poorly controlled blood pressure while visiting hypertensive patients.
Frozen sections in decision-making regarding the axillary procedures in breast conserving surgery for intraductal carcinoma at preoperative diagnosis
Authors: Kim Sanghwa , Lee Kwanbum , Alshahrani Mushabab Ali , Ahn Jee Hyun , Lee Jeea , Park Hyung Seok 
Published: August 2022

Abstract
Background: Axillary evaluation is unnecessary for pure ductal carcinoma in situ (DCIS); however, it is performed because of upstaging risks. Purpose of this study is to decrease the upstaging rate to invasive cancer and unnecessary axillary evaluation in patients with preoperative DCIS. Methods: We reviewed patients with preoperative DCIS who underwent breast-conserving surgery (BCS) with IOF biopsy. Positive Intra-operative frozen section (IOF) biopsy findings were defined as the presence of invasive or micro-invasive cancer. The IOF biopsy and permanent pathology findings were compared. Result: Seventy-eight patients underwent BCS with IOF biopsy. Six patients showed positive IOF biopsy findings; five of these patients showed concordant permanent pathology findings. Sentinel lymph node biopsy (SLNB) was positive in one patient. Thirteen patients with invasive breast cancer were not diagnosed with IOF biopsy; they underwent SLNB during the second surgery. None of them had metastatic lymph nodes. The sensitivity and specificity of IOF biopsy were 27.7% and 98.3%, respectively, with 82.1% accuracy. None of the other factors showed statistically significant relationships with the permanent pathology findings, except for the IOF biopsy findings. Conclusion: IOF evaluation can aid in detecting the invasiveness of tumors in patients with preoperative DCIS.
Group B Streptococcus screening with antenatal culture and intrapartum polymerase chain reaction
Authors: GOH Marlene Samantha Sze Minn , TAN Hong Ying , NG Yan Shun , LIM Jamie Yong Qi , CHUA Amelia Zu’er , SULTANA Rehena , TOH Wuen Lynn , SHEN Cimin Vanessa , CHONG Jiaying , TAN Ilka , YEO Kee Thai , KU Chee Wai , MATHUR Manisha 
Published: August 2022

Abstract
Group B Streptococcus (GBS) is the leading cause of early-onset neonatal sepsis. This prospective cohort study aimed to determine the sensitivity and specificity of intrapartum PCR in detecting GBS colonization in comparison to antenatal culture. Patients who presented in labor or for induction of labor, ≥ 37 weeks’ gestation, with antenatal GBS swab cultures collected during routine screening within 5 weeks of delivery were recruited. A double-vaginal intrapartum swab was taken for GBS PCR assay and culture. The performance of antenatal culture and intrapartum PCR were evaluated using the corresponding intrapartum culture as the reference standard. Among 170 included participants, antenatal culture and intrapartum PCR have comparable sensitivities of 92.1% (95% confidence interval, 78.6 – 98.3) and 89.2% (74.6 – 97.0) (p=0.655) respectively. However, intrapartum PCR has a higher specificity of 79.6% (71.7 – 86.1) compared to 61.4% (52.5 – 69.7) (p<0.001) in antenatal culture. The false positive rates for intrapartum PCR (19.2%) were lower than those for antenatal culture (38.6%). Our study suggests that intrapartum PCR is a rapid and effective test to detect GBS colonization, with comparable sensitivity and superior specificity to antenatal swab culture. This strategy may reduce unnecessary intrapartum antibiotics exposure among women who are GBS negative during labor.
Rare and Heterogeneous manifestations of Leucocyte adhesion deficiency type 1: Report of two cases with diagnostic dilemmas and Novel ITGB mutation.
Authors: Anis Sabiha , Abid Aisha , Umer Sadaf- Aba , Sarfaraz Sabahat , Junejo Samina , Shahid Saba , Sultan Sajid , Rizvi Adibul Hasan 
Published: August 2022

Abstract
Background: Primary immunodeficiency disorders (PID) are rare disorders with heterogeneous manifestations, overlapping with other diseases such as autoimmunity, malignancy, and infections. This makes the diagnosis very challenging and delays management. Leucocyte adhesion defects (LAD) are a group of PIDs in which patients lack adhesion molecules on leukocytes needed for their emigration through blood vessels to the site of infection. Patients with LAD can present with diverse clinical features including severe and life-threatening infections, early in life, and the absence of pus formation around infection or inflammation. There is often delayed umbilical cord separation, omphalitis, late wound healing, and a high white blood cell count. If not recognized and managed early, can lead to life-threatening complications and death.Case Presentation:LAD 1 is characterized by a mutation in integrin subunit beta 2 (ITGB2). We report two cases of LAD1 with unusual presentations (post-circumcision excessive bleeding and granulomatous inflammation of the right eye) which were confirmed by flowcytometric analysis and genetic testing. In one case we found a novel ITGB2 mutation (c.994‒1G>C; splice site variant).Conclusions:These cases highlight the importance of a multidisciplinary approach to recognizing clues in patients with uncommon manifestations of a rare disease. This led to the proper diagnostic workup of primary immunodeficiency disorder leading to a better understanding of the disease, appropriate patient counseling, and being better equipped to deal with complications.
Efficient plasma electron accelerator driven by linearly chirped multi-10-TW laser pulses
Authors: Grigoriadis Anastasios , Andrianaki Georgia , Tazes Ioannis , Dimitriou Vasilios , Tatarakis Michael , Benis Emmanouil , Papadogiannis Nektarios 
Published: August 2022

Abstract
The temporal rearrangement of the spectral components of an ultrafast and intense laser pulse, i.e., the chirp of the pulse, offers significant possibilities for controlling its interaction with matter and plasma. In the propagation of ultra-strong laser pulses within the self-induced plasma, laser pulse chirp can play a major role in the dynamics of wakefield and plasma bubble formation, as well as in the electron injection and related electron acceleration. Here, we experimentally demonstrate the control of the generation efficiency of a relativistic electron beam, with respect to maximum electron energy, current, and reproducibility, by accurately varying the chirp value of a multi-10-TW laser pulse. We explicitly show that positively chirped laser pulses, i.e., pulses with instantaneous frequency increasing with time, accelerate electrons in the order of 100 MeV much more efficiently in comparison to unchirped or negatively chirped pulses. Corresponding Particle-In-Cell simulations strongly support the experimental results, depicting a smoother plasma bubble density distribution and electron injection conditions that favors the maximum acceleration of the electron beam, when positively chirped laser pulses are used. Our results, aside from extending the validity of similar studies reported for PW laser pulses, provide the ground for understanding the subtle dynamics of an efficient plasma electron accelerator driven by chirped laser pulses.
Comparison of the evolutionary phylodynamic of Delta and Omicron variants of SARS-CoV-2
Authors: benazi nabil , Bounab Sabrina 
Published: August 2022

Abstract
Due to the inconsistency of the information regarding the evolution of the last two waves caused by the Delta and Omicron variants, we are attempting to provide a phylodynamic analysis. We used the nucleotide sequences of the Delta (n = 89) and Omicron (n = 74) variants recorded in the GISAID database to perform an analysis based on the contemporary model of the birth-death horizon. An average rate of evolution of 3.677 × 10− 4 subs /site/year (range,1.311× 10− 4−6.144×10− 4 ) for the DELTA variant, this gives an estimated mean of tMRCA corresponding to the root of the tree dated at 43.5 days. While for OMICRON a mean evolutionary rate of 3.898×10 − 3 subs/site/year (range,2.686×10− 3 − 5.102×10− 3) gave an estimated mean of tMRCA corresponding to the root of the tree dated at 26.4 days. The median of Re for the Indian DELTA = 1.81 (range, 0.196–3.94), and increased to 3.837 ≈ 4 on March 30, 2021. While for the South African OMICRON Re = 0.97 (range,0.41–1.54), and rose to 9.59 ≈ 9 on December 14, 2021. The average doubling times of the two waves are estimated respectively at 9 days for the DELTA variant and at 3 days for the OMICRON variant. The spread of the OMICRON pandemic is almost three times faster than that of the DELTA. The mean doubling times of the two waves are 9 days for the DELTA variant and 3 days for the OMICRON variant, respectively. As a result, the OMICRON pandemic is spreading nearly three times faster than the DELTA.
Altered dynamics of glymphatic flow in a mature-onset Tet-off APP mouse model of amyloidosis
Authors: Ben-Nejma Inès R. H. , Keliris Aneta J. , Vanreusel Verdi , Ponsaerts Peter , Linden Annemie Van der , Keliris Georgios A. 
Published: August 2022

Abstract
Background
Alzheimer’s disease (AD) is an incurable neurodegenerative disorder characterised by the progressive build-up of toxic amyloid-beta (Aβ) and tau protein aggregates eventually leading to cognitive decline. Recent lines of evidence suggest that an impairment of the glymphatic system (GS), a brain waste clearance pathway, plays a key role in the pathology of AD. Moreover, a relationship between GS function and neuronal network integrity has been strongly implicated. Here, we sought to assess the efficacy of the GS in a transgenic Tet-off mouse model of amyloidosis, in which the expression of mutant APP was delayed until maturity, mimicking features of late-onset AD – the most common form of dementia in humans.
Methods
To evaluate GS function, we used dynamic contrast enhanced MRI (DCE-MRI) in 14-months-old Tet-Off APP (AD) mice and aged-matched littermate controls. Brain-wide transport of Gd-DOTA contrast agent was monitored over time after cisterna magna injection. Region of interest analysis and computational modelling were used to assess GS dynamics while characterisation of brain tissue abnormalities at the microscale was performed ex vivo by immunohistochemistry.
Results
We observed reduced rostral glymphatic flow and higher accumulation of contrast agent in areas proximal to the injection side in the AD group. Clustering and subsequent computational modelling of voxel time courses revealed significantly lower inflow time constants in AD relative to the controls. Ex vivo evaluation showed abundant amyloid plaque burden in the AD group coinciding with extensive astrogliosis and microgliosis. The neuroinflammatory responses were also found in plaque-devoid regions, potentially impacting brain fluid circulation.
Conclusions
In a context resembling late-onset AD in humans, we demonstrate the disruption of glymphatic function and particularly a reduction in brain-fluid inflow in the AD group. We conjecture that the hindered circulation of cerebrospinal fluid is potentially caused by wide-spread astrogliosis and amyloid-related obstruction of the normal routes of glymphatic flow resulting in redirection towards caudal regions. In sum, our study highlights the translational potential of alternative approaches, such as targeting brain fluid circulation as potential therapeutic strategies for AD.
Predicting efficacy of drug-carrier nanoparticle designs for cancer treatment – A machine learning-based solution
Authors: Kibria Md Raisul , Akbar Refo Ilmiya , Nidadavolu Poonam , Havryliuk Oksana , Lafond Sébastien , Azimi Sepinoud 
Published: August 2022

Abstract
Molecular Dynamic (MD) simulations are very effective in the discovery of nanomedicines for treating cancer, but these are computationally expensive and time-consuming. Existing studies integrating machine learning (ML) into MD simulation to enhance the process and enable efficient analysis cannot provide direct insights without the complete simulation. In this study, we present an ML-based approach for predicting the solvent accessible surface area (SASA) of a nanoparticle (NP), denoting its efficacy, from a fraction of the MD simulations data. The proposed framework uses a time series model for simulating the MD, resulting in an intermediate state, and a second model to calculate the SASA in that state. Empirically, the solution can predict the SASA value 260 timesteps ahead 7.5 times faster with a very low average error of 1956.93. We also introduce the use of an explainability technique to validate the predictions. This work can reduce the computational expense of both processing and data size greatly while providing reliable solutions for the nanomedicine design process.