bluuebunny/crossref_metadata_2025 huggingface dataset:
A hypothesis to derive the shape of the dose–response curve for teratogenic radiation effects
Authors: Körblein Alfred
Published: February 2022

Reports of adverse pregnancy outcomes after in utero exposure to very low levels of ionizing radiation are inconsistent with a threshold dose of 100 mSv for teratogenic effects in humans. In the present study, it is hypothesized that the shape of the dose–response relationship for teratogenic effects is a cumulative lognormal distribution without threshold. This hypothesis relies on the assumption that both doses and radiosensitivities in human populations exposed to ionizing radiation are random variables, modeled by lognormal density functions. Here, radiosensitivity is defined as the dose limit up to which radiation damage can be repaired by the cellular repair systems, in short, the repair capacity. Monte Carlo simulation is used to generate N pairs of individual doses and repair capacities. Radiation damage occurs whenever the dose exceeds the related repair capacity. The rate of radiation damage is the number of damages, divided by the number N of pairs. Monte Carlo simulation is conducted for a sufficient number of ascending median doses. The shape of the dose–response relationship is determined by regression of damage rates on mean dose. Regression with a cumulative lognormal distribution function yields a perfect fit to the data. Acceptance of the hypothesis means that studies of adverse health effects following in-utero exposure to low doses of ionizing radiation should not be discarded primarily because they contradict the concept of a threshold dose for teratogenic effects.
Human spatial memory is biased towards high-calorie foods: a cross-cultural online experiment
Authors: de Vries Rachelle , Boesveldt Sanne , de Vet Emely
Published: February 2022

Background

Human memory appears to prioritise locations of high-calorie foods, likely as an adaptation for foraging within fluctuating ancestral food environments. Importantly, this “high-calorie bias” in human spatial memory seems to yield consequences for individual eating behaviour in modern food-abundant settings. However, as studies have mainly been conducted in European (Dutch) populations to date, we investigated whether the existence of the cognitive bias can be reasonably generalised across countries that vary on culturally-relevant domains, such as that of the USA and Japan. Furthermore, we investigated whether sociodemographic factors moderate the expression of the high-calorie spatial memory bias in different populations.

Methods

In a cross-cultural online experiment, we measured the food location memory of diverse participants from the USA (N = 72; 44.4% Male; 54 ± 15.99 years) and Japan (N = 74; 56.8% Male; 50.85 ± 17.32 years), using a validated computer-based spatial memory task with standardised images of high-calorie and low-calorie foods. To directly compare the magnitude of the high-calorie spatial memory bias in a broader cultural scope, we also included data from a previous online experiment that identically tested the food spatial memory of a Dutch sample (N = 405; 56.7% Male; 47.57 ± 17.48 years).

Results

In the US sample, individuals more accurately recalled (i.e. had lower pointing errors for) locations of high-calorie foods versus that of low-calorie alternatives (Mean difference = -99.23 pixels, 95% CI = [-197.19, -1.28]) – regardless of one’s hedonic preferences, familiarity with foods, and encoding times. Likewise, individuals in the Japanese sample displayed an enhanced memory for locations of high-calorie (savoury-tasting) foods (Mean difference = -40.41 pixels, 95% CI = [-76.14, -4.68]), while controlling for the same set of potential confounders. The magnitude of the high-calorie bias in spatial memory was similar across populations (i.e. the USA, Japan, and the Netherlands), as well as across diverse sociodemographic groups within a population.

Conclusions

Our results demonstrate that the high-calorie bias in spatial memory transcends sociocultural boundaries. Since the cognitive bias may negatively impact on our dietary decisions, it would be wise to invest in strategies that intervene on our seemingly universal ability to efficiently locate calorie-rich foods.
B-cell maturation antigen targeting strategies in multiple myeloma treatment, advantages and disadvantages
Authors: Nobari Shirin Teymouri , Nojadeh Jafar Nouri , Talebi Mehdi
Published: February 2022

B cell maturation antigen (BCMA), a transmembrane glycoprotein member of the tumor necrosis factor receptor superfamily 17 (TNFRSF17), highly expressed on the plasma cells of Multiple myeloma (MM) patients, as well as the normal population. BCMA is used as a biomarker for MM. Two members of the TNF superfamily proteins, including B-cell activating factor (BAFF) and A proliferation-inducing ligand (APRIL), are closely related to BCMA and play an important role in plasma cell survival and progression of MM. Despite the maximum specificity of the monoclonal antibody technologies, introducing the tumor-specific antigen(s) is not applicable for all malignancies, such as MM that there plenty of relatively specific antigens such as GPCR5D, MUC1, SLAMF7 and etc., but higher expression of BCMA on these cells in comparison with normal ones can be regarded as a relatively exclusive marker. Currently, different monoclonal antibody (mAb) technologies applied in anti-MM therapies such as daratuzumab, SAR650984, GSK2857916, and CAR-T cell therapies are some of these tools that are reviewed in the present manuscript. By the way, the structure, function, and signaling of the BCMA and related molecule(s) role in normal plasma cells and MM development, evaluated as well as the potential side effects of its targeting by different CAR-T cells generations. In conclusion, BCMA can be regarded as an ideal molecule to be targeted in immunotherapeutic methods, regarding lower potential systemic and local side effects.
Serine, N-acetylaspartate differentiate adolescents with juvenile idiopathic arthritis compared with healthy controls: a metabolomics cross-sectional study
Authors: Lewis Kimberly A. , Osier Nico , Carrasco Ruy , Chiou Jennifer , Carter Patricia , Garcia Alexandra , Flowers Elena , Gennatas Efstathios D. , Nguyen Christina , Rana Ambreen , Brown Sharon A. , Tiziani Stefano
Published: February 2022

Background

In comparison with the general population, adolescents with juvenile idiopathic arthritis (JIA) are at higher risk for morbidity and mortality. However, limited evidence is available about this condition’s underlying metabolic profile in adolescents with JIA relative to healthy controls. In this untargeted, cross-sectional metabolomics study, we explore the plasma metabolites in this population.

Methods

A sample of 20 adolescents with JIA and 20 controls aged 13–17 years were recruited to complete surveys, provide medical histories and biospecimens, and undergo assessments. Fasting morning plasma samples were processed with liquid chromatography–mass spectrometry. Data were centered, scaled, and analyzed using generalized linear models accounting for age, sex, and medications (p-values adjusted for multiple comparisons using the Holm method). Spearman’s correlations were used to evaluate relationships among metabolites, time since diagnosis, and disease severity.

Results

Of 72 metabolites identified in the samples, 55 were common to both groups. After adjustments, 6 metabolites remained significantly different between groups. Alpha-glucose, alpha-ketoglutarate, serine, and N-acetylaspartate were significantly lower in the JIA group than in controls; glycine and cystine were higher. Seven additional metabolites were detected only in the JIA group; 10 additional metabolites were detected only in the control group. Metabolites were unrelated to disease severity or time since diagnosis.

Conclusions

The metabolic signature of adolescents with JIA relative to controls reflects a disruption in oxidative stress; neurological health; and amino acid, caffeine, and energy metabolism pathways. Serine and N-acetylaspartate were promising potential biomarkers, and their metabolic pathways are linked to both JIA and cardiovascular disease risk. The pathways may be a source of new diagnostic, treatment, or prevention options. This study’s findings contribute new knowledge for systems biology and precision health approaches to JIA research. Further research is warranted to confirm these findings in a larger sample.
Pulmonary large cell carcinoma with neuroendocrine morphology shows genetic similarity to large cell neuroendocrine carcinoma
Authors: Liang Zuoyu , Wang Weiya , Hu Qianrong , Zhou Ping , Zhang Ying , Tang Yuan , Wu Qian , Fu Yiyun , Li Xue , Shao Yang , Jiang Lili
Published: February 2022

Background

Large cell neuroendocrine carcinoma (LCNEC) is a high-grade malignant pulmonary neuroendocrine tumour. The distinction of pulmonary large cell carcinoma (LCC) and LCNEC is based on the presence of neuroendocrine morphology and the expression of at least one neuroendocrine marker in at least 10% of tumour cells in the latter. According to the current classification, LCC with neuroendocrine morphology and without neuroendocrine marker expression is classified as LCC. This subgroup we have named LCNEC-null and aimed to analyze its characteristics.

Methods

31 surgical samples resected in West China Hospital of Sichuan University between 2017 to 2021 were collected, including 7 traditional LCCs, 11 LCNEC-nulls and 13 LCNECs. Each case was conducted to immunohistochemistry and 425-panel-NGS.

Results

Compared to other LCCs, detailed analysis of LCNEC-nulls revealed biological features similar to those of LCNECs, especially for immunohistochemistry and molecular analysis: 1. diffusive, coarse granular and high expression of Pan-CK; 2. rare PD-L1 expression; 3. High rate of p53 expression and Rb deficiency 4. abundant genetic alterations are similar to LCNEC. All characteristics above deviated from traditional LCC, indicating they have the same origin as LCNEC. Furthermore, LCNEC could be genetically divided into two subtypes when we reclassified LCNEC-null as LCNEC, and the mutational type and prognosis differed significantly.

Conclusions

We consider that LCNEC-null should be reclassified as LCNEC based on analysis above. In addition, two genetic types of LCNEC with different prognosis also indicate two mechanism of tumour formation.
Factors associated with long-term survival in gemcitabine-concurrent proton radiotherapy for non-metastatic locally advanced pancreatic cancer: a single-center retrospective study
Authors: Ogura Yuta , Terashima Kazuki , Nanno Yoshihide , Park SungChul , Suga Masaki , Takahashi Daiki , Matsuo Yoshiro , Sulaiman Nor Shazrina , Tokumaru Sunao , Okimoto Tomoaki , Toyama Hirochika , Fukumoto Takumi
Published: February 2022

Background

Factors associated with long-term survival in gemcitabine-concurrent proton radiotherapy (GPT) for non-metastatic, locally advanced pancreatic cancer (LAPC) remain unclear. This study aimed to determine the factors associated with long-term survival in GPT for non-metastatic LAPC.

Methods

The medical records of 123 patients with LAPC treated with GPT between February 2009 and December 2019 at Hyogo Ion Beam Medical Center were retrospectively reviewed to assess the factors associated with long-term survival outcomes.

Results

The median overall survival of the total cohort treated with GPT was 18.7 months. The 1- and 2-year overall, local progression-free, and progression-free survival rates were 70.4% and 35.7%, 78.2% and 59.0%, and 38.6% and 20.8%, respectively. Multivariate analysis revealed that LAPCs at the pancreatic body-tail and those without anterior peripancreatic invasion were independently associated with longer overall survival (P = 0.040 and P = 0.015, respectively). The median overall survival of patients with LAPC at the pancreatic body-tail and those with LAPC without anterior peripancreatic invasion were 24.1 and 28.1 months, respectively. LAPCs at the pancreatic body-tail had a higher volume ratio irradiated over 60 Gy equivalents at gross tumor volume than those at the pancreatic head (P < 0.001). LAPCs with anterior peripancreatic invasion had more peritoneal recurrence within 6 months after GTP than those without anterior peripancreatic invasion (P = 0.039).

Conclusions

GPT is a promising treatment option for patients with LAPC at the pancreatic body-tail and those with LAPC without anterior peripancreatic invasion.
Awareness and agreement with neurofibromatosis care guidelines among U.S. neurofibromatosis specialists
Authors: Merker Vanessa L. , Knight Pamela , Radtke Heather B. , Yohay Kaleb , Ullrich Nicole J. , Plotkin Scott R. , Jordan Justin T.
Published: February 2022

Introduction

The neurofibromatoses (NF) are a group of rare, genetic diseases sharing a predisposition to develop multiple benign nervous system tumors. Given the wide range of NF symptoms and medical specialties involved in NF care, we sought to evaluate the level of awareness of, and agreement with, published NF clinical guidelines among NF specialists in the United States.

Methods

An anonymous, cross-sectional, online survey was distributed to U.S.-based NF clinicians. Respondents self-reported demographics, practice characteristics, awareness of seven NF guideline publications, and level of agreement with up to 40 individual recommendations using a 5-point Likert scale. We calculated the proportion of recommendations that each clinician rated “strongly agree”, and assessed for differences in guideline awareness and agreement by respondent characteristics.

Results

Sixty-three clinicians (49% female; 80% academic practice) across > 8 medical specialties completed the survey. Awareness of each guideline publication ranged from 53%-79% of respondents; specialists had higher awareness of publications endorsed by their medical professional organization (p < 0.05). The proportion of respondents who “strongly agree” with individual recommendations ranged from 17%-83%; for 16 guidelines, less than 50% of respondents “strongly agree”. There were no significant differences in overall agreement with recommendations based on clinicians’ gender, race, specialty, years in practice, practice type (academic/private practice/other), practice location (urban/suburban/rural), or involvement in NF research (p > 0.05 for all).

Conclusions

We identified wide variability in both awareness of, and agreement with, published NF care guidelines among NF experts. Future quality improvement efforts should focus on evidence-based, consensus-driven methods to update and disseminate guidelines across this multi-specialty group of providers. Patients and caregivers should also be consulted to proactively anticipate barriers to accessing and implementing guideline-driven care. These recommendations for improving guideline knowledge and adoption may also be useful for other rare diseases requiring multi-specialty care coordination.
Diagnostic value of fetal hemoglobin Bart’s for evaluation of fetal α-thalassemia syndromes: application to prenatal characterization of fetal anemia caused by undiagnosed α-hemoglobinopathy
Authors: Singha Kritsada , Yamsri Supawadee , Chaibunruang Attawut , Srivorakun Hataichanok , Sanchaisuriya Kanokwan , Fucharoen Goonnapa , Fucharoen Supan
Published: February 2022

Background

To evaluate whether the quantification of fetal hemoglobin (Hb) Bart’s is useful for differentiation of α-thalassemia syndromes in the fetus and to characterize the fetal anemia associated with fetal α-hemoglobinopathy.

Methods

A total of 332 fetal blood specimens collected by cordocentesis were analyzed using capillary electrophoresis and the amount of Hb Bart’s was recorded. The result was evaluated against thalassemia genotypes determined based on Hb and DNA analyses. Prenatal Hb and DNA characterization of the fetal anemia observed in two families was done.

Results

Among 332 fetuses investigated, Hb and DNA analyses identified 152 fetuses with normal genotypes. The remaining 180 fetuses carried α-thalassemia with several genotypes. Variable amounts of Hb Bart’s were identified in all fetuses with α-thalassemia, which could be used for simple differentiation of fetal α-thalassemia genotypes. These included α+- and α0-thalassemia traits, homozygous α+-thalassemia and Hb Constant Spring (CS), Hb H disease, Hb H-CS and Hb H-Quong Sze diseases, homozygous α0-thalassemia causing the Hb Bart’s hydrops fetalis and a remain uncharacterized α-thalassemia defect. The previously undescribed interactions of Hb Queens Park and Hb Amsterdam A1 with Hb E were detected in two fetuses with Hb Bart’s of 0.5%. The Hb Queens Park-AEBart’s disease was also noted in one pregnant woman. Prenatal analysis of the fetuses with severe fetal anemia and cardiomegaly with Hb Bart’s of 9.0% and 13.6% revealed unexpectedly the homozygous Hb CS and a compound heterozygosity of Hb CS/Hb Pakse’ with Hb E heterozygote, respectively.

Conclusions

The usefulness of detecting and differentiation of fetal α-thalassemia syndromes by quantifying of Hb Bart’s was demonstrated. Apart from the fatal condition of Hb Bart’s hydrops fetalis associated with homozygous α0-thalassemia, homozygous Hb CS and a compound Hb CS/Hb Pakse’ could result in severe fetal anemia and fetal complications, prenatal diagnosis is highly recommended. The simple Hb Bart’s quantification of fetal blood should prove helpful in this matter.
iSuc-ChiDT: a computational method for identifying succinylation sites using statistical difference table encoding and the chi-square decision table classifier
Authors: Zeng Ying , Chen Yuan , Yuan Zheming
Published: February 2022

Background

Lysine succinylation is a type of protein post-translational modification which is widely involved in cell differentiation, cell metabolism and other important physiological activities. To study the molecular mechanism of succinylation in depth, succinylation sites need to be accurately identified, and because experimental approaches are costly and time-consuming, there is a great demand for reliable computational methods. Feature extraction is a key step in building succinylation site prediction models, and the development of effective new features improves predictive accuracy. Because the number of false succinylation sites far exceeds that of true sites, traditional classifiers perform poorly, and designing a classifier to effectively handle highly imbalanced datasets has always been a challenge.

Results

A new computational method, iSuc-ChiDT, is proposed to identify succinylation sites in proteins. In iSuc-ChiDT, chi-square statistical difference table encoding is developed to extract positional features, and has a higher predictive accuracy and fewer features compared to common position-based encoding schemes such as binary encoding and physicochemical property encoding. Single amino acid and undirected pair-coupled amino acid composition features are supplemented to improve the fault tolerance for residue insertions and deletions. After feature selection by Chi-MIC-share algorithm, the chi-square decision table (ChiDT) classifier is constructed for imbalanced classification. With a training set of 4748:50,551(true: false sites), ChiDT clearly outperforms traditional classifiers in predictive accuracy, and runs fast. Using an independent testing set of experimentally identified succinylation sites, iSuc-ChiDT achieves a sensitivity of 70.47%, a specificity of 66.27%, a Matthews correlation coefficient of 0.205, and a global accuracy index Q9 of 0.683, showing a significant improvement in sensitivity and overall accuracy compared to PSuccE, Success, SuccinSite, and other existing succinylation site predictors.

Conclusions

iSuc-ChiDT shows great promise in predicting succinylation sites and is expected to facilitate further experimental investigation of protein succinylation.
Identifying targets for increased biogas production through chemical and organic matter characterization of digestate from full-scale biogas plants: what remains and why?
Authors: Ekstrand Eva-Maria , Björn Annika , Karlsson Anna , Schnürer Anna , Kanders Linda , Yekta Sepehr Shakeri , Karlsson Martin , Moestedt Jan
Published: February 2022

Background

This study examines the destiny of macromolecules in different full-scale biogas processes. From previous studies it is clear that the residual organic matter in outgoing digestates can have significant biogas potential, but the factors dictating the size and composition of this residual fraction and how they correlate with the residual methane potential (RMP) are not fully understood. The aim of this study was to generate additional knowledge of the composition of residual digestate fractions and to understand how they correlate with various operational and chemical parameters. The organic composition of both the substrates and digestates from nine biogas plants operating on food waste, sewage sludge, or agricultural waste was characterized and the residual organic fractions were linked to substrate type, trace metal content, ammonia concentration, operational parameters, RMP, and enzyme activity.

Results

Carbohydrates represented the largest fraction of the total VS (32–68%) in most substrates. However, in the digestates protein was instead the most abundant residual macromolecule in almost all plants (3–21 g/kg). The degradation efficiency of proteins generally lower (28–79%) compared to carbohydrates (67–94%) and fats (86–91%). High residual protein content was coupled to recalcitrant protein fractions and microbial biomass, either from the substrate or formed in the degradation process. Co-digesting sewage sludge with fat increased the protein degradation efficiency with 18%, possibly through a priming mechanism where addition of easily degradable substrates also triggers the degradation of more complex fractions. In this study, high residual methane production (> 140 L CH4/kg VS) was firstly coupled to operation at unstable process conditions caused mainly by ammonia inhibition (0.74 mg NH3-N/kg) and/or trace element deficiency and, secondly, to short hydraulic retention time (HRT) (55 days) relative to the slow digestion of agricultural waste and manure.

Conclusions

Operation at unstable conditions was one reason for the high residual macromolecule content and high RMP. The outgoing protein content was relatively high in all digesters and improving the degradation of proteins represents one important way to increase the VS reduction and methane production in biogas plants. Post-treatment or post-digestion of digestates, targeting microbial biomass or recalcitrant protein fractions, is a potential way to achieve increased protein degradation.
Assessment of source material for human intestinal organoid culture for research and clinical use
Authors: Urbano Paulo C. M. , Angus Hamish C. K. , Gadeock Safina , Schultz Michael , Kemp Roslyn A.
Published: February 2022

Objective

Human intestinal organoids (hIOs) have potential as a model for investigating intestinal diseases. The hIO system faces logistic challenges including limited access to biopsies or low expression of epithelial cell types. Previous research identified the feasibility of tissue from the transverse (TC) or sigmoid colon (SC), or from cryopreserved biopsies from regions of the gastrointestinal tract. We aimed to create a protocol for robust hIO generation that could be implemented across multiple centres, allowing for development of a consistent biobank of hIOs from diverse patients.

Results

TC and SC hIOs were expanded from fresh or frozen biopsies with standard or refined media. The expression of epithelial cells was evaluated via PCR. Growth of TC and SC hIO from healthy donors was reproducible from freshly acquired and frozen biopsies. A refined media including insulin-like growth factor (IGF)-1 and fibroblast growth factor (FGF)-2 enabled the expression of epithelial cells, including higher expression of goblet cells and enterocytes compared to standard organoid media. We identified a consistent time point where hIOs generated from frozen biopsies reflect similar hIO composition from freshly acquired samples. Feasibility of hIOs as a tool for research and clinical use, including the use of frozen biopsies, was demonstrated.
Difference in the prevalence of hypertension and its risk factors depending on area-level deprivation in Japan
Authors: Okui Tasuku , Park Jinsang
Published: February 2022

Objectives

Area-level deprivation is an important factor related to mortality or health behaviors; however, a study investigating differences in hypertension prevalence depending on area-level deprivation has not been conducted in Japan. We investigated differences in the prevalence of hypertension and its risk factors, i.e. obesity, smoking, alcohol consumption, and heavy alcohol drinking depending on area-level deprivation using nationwide health checkups data in 2018.

Results

Area-level deprivation was derived from census data. An analysis of the data by secondary medical areas revealed that the age-standardized proportions of individuals whose systolic blood pressure was ≥ 140 mmHg, those whose diastolic blood pressure was ≥ 90 mmHg, those whose body mass index was ≥ 25 or 30 kg/m2, smokers, and heavy alcohol drinkers showed an increasing trend with an increase in the deprivation level. The relative index of inequality, which can be interpreted as the ratio of the age-standardized proportion for the most deprived area compared with that for the least deprived area, was significantly greater than 1 for all proportions, except for the proportion of drinkers in women. Overall, there was a disparity in the prevalence of hypertension and its risk factors depending on area-level deprivation.
Very low concentration of lipopolysaccharide can induce the production of various cytokines and chemokines in human primary monocytes
Authors: Chaiwut Ratthakorn , Kasinrerk Watchara
Published: February 2022

Objective

Lipopolysaccharide (LPS), a component of gram-negative bacteria, is a potent innate immune stimulus. The interaction of LPS with innate immune cells induces the production of proinflammatory cytokines and chemokines, thereby leading to the control of infection. In the present study, we investigated the effect of a wide range of LPS concentrations on the regulation of various proinflammatory cytokines and chemokines in human primary monocytes and T lymphocytes.

Results

We demonstrated that a very low concentration of LPS could regulate the production of cytokines and chemokines in monocytes but not T lymphocytes. Unexpectedly, very low concentrations of LPS (0.0025 and 0.005 ng/mL) could induce TNF-α and IL-6 production, respectively, in monocytes. Our findings provide evidence that in the presence of monocytes, even very low endotoxin contamination could induce cytokine production. We suggest that the recombinant proteins used to investigate immune functions must be thoroughly screened for endotoxins using a highly sensitive method.
Chronic inflammatory demyelinating polyneuropathy with anti-contactin-associated protein 1 antibody and bile duct hamartomas in the liver: a case report
Authors: Hu Shurong , Hu Yin , Du Qiang
Published: February 2022

Background

Autoantibodies targeting node of Ranvier proteins are rarely reported in China.

Case presentation

We present the case of a 66-year-old Chinese man who concomitantly developed chronic inflammatory demyelinating polyneuropathy with anti-contactin-associated protein 1 antibody and bile duct hamartomas in liver, which are rarely reported in China. The man presented with chronic progressive sensory and motor symptoms, bilateral periphery facial paralysis, and protein–cell dissociation of cerebrospinal fluid. Nerve conduction study indicated demyelinating neuropathy. Enhanced magnetic resonance imaging of the liver showed diffuse intrahepatic lesions, which were considered as bile duct hamartomas in the liver. He was suspected as having chronic inflammatory demyelinating polyneuropathy and treated with intravenous immunoglobulin and prednisone. However, his condition got worse. One month later, he was diagnosed with chronic inflammatory demyelinating polyneuropathy associated with anti-contactin-associated protein 1 antibody. He received high-dose methylprednisolone, followed by standard plasma exchange and rituximab therapy. His sensory and motor manifestations were significantly improved at 1 year of follow-up.

Conclusions

This case reminds clinicians to be aware of antiparanodal antibodies, which are associated with specific phenotypes and therapeutic response.
A deep adversarial model for segmentation-assisted COVID-19 diagnosis using CT images
Authors: Yao Hai-yan , Wan Wang-gen , Li Xiang
Published: February 2022

The outbreak of coronavirus disease 2019 (COVID-19) is spreading rapidly around the world, resulting in a global pandemic. Imaging techniques such as computed tomography (CT) play an essential role in the diagnosis and treatment of the disease since lung infection or pneumonia is a common complication. However, training a deep network to learn how to diagnose COVID-19 rapidly and accurately in CT images and segment the infected regions like a radiologist is challenging. Since the infectious area is difficult to distinguish manually annotation, the segmentation results are time-consuming. To tackle these problems, we propose an efficient method based on a deep adversarial network to segment the infection regions automatically. Then, the predicted segment results can assist the diagnostic network in identifying the COVID-19 samples from the CT images. On the other hand, a radiologist-like segmentation network provides detailed information of the infectious regions by separating areas of ground-glass, consolidation, and pleural effusion, respectively. Our method can accurately predict the COVID-19 infectious probability and provide lesion regions in CT images with limited training data. Additionally, we have established a public dataset for multitask learning. Extensive experiments on diagnosis and segmentation show superior performance over state-of-the-art methods.
Effects of nightlife activities on urban spaces and design: a case study of Cairo, Egypt
Authors: Elshater Abeer , Abusaada Hisham
Published: February 2022

Hyper-diversity in old communities should be rehabilitated to address various man-made changes that threaten sustainability and viability at night. This study elucidates this argument by reviewing and synthesising theoretical and empirical evidence about urban governance support regarding the participation of neighbourhood residents to improve or eliminate nightlife. The method is based on a systematic review, direct observation and interview with random samples of residents, workers and visitors in commercial and recreational places. This study criticises changes in the public space of the Al-Hussein Mosque, which led to changes in urban forms and affected the nightlife in Old Cairo. However, it asserts that the hyper-diversity of activities in public spaces because of the lack of urban governance controls should consider changes in terms of the participation of vulnerable groups in nightlife. A new conceptual framework for interpreting stakeholders’ positive and negative responses is proposed, which operates across four overlapping steps of urban governance: predicting, proposing, preparing and preventing.
Semantic context driven language descriptions of videos using deep neural network
Authors: Naik Dinesh , Jaidhar C. D.
Published: February 2022

The massive addition of data to the internet in text, images, and videos made computer vision-based tasks challenging in the big data domain. Recent exploration of video data and progress in visual information captioning has been an arduous task in computer vision. Visual captioning is attributable to integrating visual information with natural language descriptions. This paper proposes an encoder-decoder framework with a 2D-Convolutional Neural Network (CNN) model and layered Long Short Term Memory (LSTM) as the encoder and an LSTM model integrated with an attention mechanism working as the decoder with a hybrid loss function. Visual feature vectors extracted from the video frames using a 2D-CNN model capture spatial features. Specifically, the visual feature vectors are fed into the layered LSTM to capture the temporal information. The attention mechanism enables the decoder to perceive and focus on relevant objects and correlate the visual context and language content for producing semantically correct captions. The visual features and GloVe word embeddings are input into the decoder to generate natural semantic descriptions for the videos. The performance of the proposed framework is evaluated on the video captioning benchmark dataset Microsoft Video Description (MSVD) using various well-known evaluation metrics. The experimental findings indicate that the suggested framework outperforms state-of-the-art techniques. Compared to the state-of-the-art research methods, the proposed model significantly increased all measures, B@1, B@2, B@3, B@4, METEOR, and CIDEr, with the score of 78.4, 64.8, 54.2, and 43.7, 32.3, and 70.7, respectively. The progression in all scores indicates a more excellent grasp of the context of the inputs, which results in more accurate caption prediction.
Semen collection, evaluation, and cryopreservation in the bonobo (Pan paniscus)
Authors: Gerits Ilse , Wydooghe Eline , Peere Sofie , Vercammen Francis , Stevens Jeroen M. G. , Ververs Cyriel
Published: February 2022

Background

Captive breeding of bonobos (Pan paniscus)has proven to be successful, but maintaining genetic diversity remains a challenge. Cryopreservation of semen is an important potential tool to maintain genetic diversity by preserving current genetic material for future use, as well as facilitating the transport and exchange of genetic material. This study aimed to develop a protocol for semen collection and cryopreservation in the bonobo. Semen was collected from four healthy adult bonobos under general anesthesia during management translocation procedures. Semen collection utilizing urethral catheterization was not successful (n = 1), however, all males (n = 4) responded well to rectal probe electro-ejaculation. Immediately after collection, ejaculates were evaluated for color and admixtures, volume, motility, and concentration. Eosin-Nigrosin staining was prepared to evaluate morphology and viability. Ejaculates were split into two equal volumes and cryopreserved in two different extenders, using a one-step and a two-step approach. Ejaculates were gradually cooled to 4 °C in two hours, subsequently stored in liquid nitrogen vapor for twenty minutes (0.25 ml straws), and finally dropped into liquid nitrogen.

Results

Pre-freeze evaluation showed thick, white samples with an average ejaculate volume of 450 µl (100-1000 µl), total motility of 59% (40–80%), viability of 69% (38–85%) and 58% (46–72%) normal spermatozoa. Mainly head (22%) and tail (19%) defects were detected on the Eosin-Nigrosin stain. Ejaculates were highly concentrated, nevertheless, due to the coagulum that caused high viscosity and non-homogenous fractions, only estimations of concentration could be made (1000 million/ml). After 24 h of storage, the post-thaw evaluation showed a loss of quality with an average post-thaw total motility of 15% (5–25%) using the one-step freezing medium, and 19% (5–30%) using the two-step medium. Average post-thaw viability was 15% (4–24%) and 21% (15–29%), respectively.

Conclusions

This report on ejaculates from bonobos obtained by rectal probe electro-ejaculation shows that semen parameters of this species are not completely similar to those of its sibling species, the chimpanzee. Further studies are necessary to develop an optimal protocol for the processing and cryopreservation of bonobo spermatozoa.
Entrepreneurial, institutional and financial strategies for FinTech profitability
Authors: Carbó-Valverde Santiago , Cuadros-Solas Pedro J. , Rodríguez-Fernández Francisco
Published: February 2022

Notwithstanding the emergence of FinTech startups in the financial services industry, most of these companies face significant difficulties in breaking even and surviving. This study examines the main managerial, institutional, and financial drivers of FinTech profitability and the time it takes for these firms to break even. The database includes relevant qualitative factors, such as foundational characteristics, the technological profile of the startup, and its funding structure. Using the full population of FinTech startups operating in Spain from 2005 to 2017, we observe that most of these firms are unprofitable within three years of their inception. Combining panel data and survival analyses, we empirically find that large and solvent FinTech firms founded by single entrepreneurs in an incubator or accelerator program are more likely to be profitable and prevail. FinTech firms reach their break-even points faster if they receive funding through seed capital.
Vasoconstriction and hyperperfusion syndrome after carotid artery stenting
Authors: Kobayashi Yuya , Morizumi Teruya , Okumura Gaku , Nagamatsu Kiyoshiro , Shimizu Yusaku , Sasaki Tetsuo , Sato Atsushi
Published: February 2022

Background

Common complications of carotid artery stenting (CAS) are cerebral ischemia and hyperperfusion syndrome. To date, only a few cases of late-onset cerebral vasoconstriction occurring several hours after CAS have been reported. However, there are no reports of developed vasoconstriction and hyperperfusion syndrome.

Case presentation

A 79-year-old man developed vasoconstriction 1 day after carotid artery stenting. Vasoconstriction improved immediately with glucocorticoid. However, a week later, the patient developed hyperperfusion syndrome.

Conclusions

Postoperative vasoconstriction and hyperperfusion syndrome is an unrecognized complication and surgeons should be aware of it.
Added value of fetal MRI as a complementary method to antenatal ultrasound in the assessment of non-CNS fetal congenital anomalies
Authors: Eshiba Samar Mohamed , Zahran Mohamed Hamdy , Elnekeidy Abdelaziz Mohamed , Abdeldayem Tamer M. , Hassan Hebatallah Hassan Mamdouh
Published: February 2022

Background

Birth defects and congenital anomalies are different words used to describe developmental abnormalities that occur at birth. Congenital anomalies diagnosis during pregnancy is a difficult topic to which ultrasonography has made significant contributions. The availability of a generally safe, independent technique in the evaluation of prenatal anomalies would be a welcomed clinical and scientific alternative. Ultrasound (US) is the predominant modality for evaluating disorders related to fetus and pregnancy. In most situations, this examination by a professional operator offers sufficient information about fetal morphology, surroundings, and well-being. The abnormalities revealed by ultrasound can be subtle or inconclusive at times. MRI has been demonstrated to be useful in such circumstances in various studies. So the effective use of fetal MRI in the evaluation of non-CNS abnormalities of the body is a reason for adopting fetal MRI as an adjunct to US in obstetric imaging. This study aimed to examine the role of fetal MRI as a complementary method to the antenatal US in assessing non-CNS anomalies and how it changed or modified the diagnosis of anomalies.

Results

By analyzing the data of 30 pregnant females with fetal non-CNS congenital anomalies, the diagnostic accuracy of prenatal ultrasound alone in the detection of congenital anomalies was 76%, with a sensitivity of about 76%. And diagnostic accuracy of MRI alone was 96.6%, with a sensitivity of approximately 96.6%. Moreover, the diagnostic accuracy of combined prenatal US and prenatal MRI in the detection of congenital anomalies was 100%, with sensitivity about 100% and PPV about 100%.

Conclusion

Fetal MRI raises confidence in non-CNS malformation assessment. Compared to US, MRI overcomes many of the obstacles faced by the antenatal US. MRI is superior to the US in refining, changing, or adding more diagnostic information about the disease.
Resequencing and genome-wide association studies of autotetraploid potato
Authors: Zhang Feng , Qu Li , Gu Yincong , Xu Zhi-Hong , Xue Hong-Wei
Published: February 2022

Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.
Kinesin motor KIFC1 is required for tubulin acetylation and actin-dependent spindle migration in mouse oocyte meiosis
Authors: Shan Meng-Meng , Zou Yuan-Jing , Pan Zhen-Nan , Zhang Hao-Lin , Xu Yi , Ju Jia-Qian , Sun Shao-Chen
Published: February 2022

Mammalian oocyte maturation is a unique asymmetric division, which is mainly because of actin-based spindle migration to the cortex. In the present study, we report that a kinesin motor KIFC1, which is associated with microtubules for the maintenance of spindle poles in mitosis, is also involved in actin dynamics in murine oocyte meiosis, co-localizing with microtubules during mouse oocyte maturation. Depletion of KIFC1 caused the failure of polar body extrusion, and we found that meiotic spindle formation and chromosome alignment were disrupted. This might be because of the effects of KIFC1 on HDAC6 and NAT10-based tubulin acetylation, which further affected microtubule stability. Mass spectroscopy analysis revealed that KIFC1 also associated with several actin nucleation factors and we found that KIFC1 was essential for the distribution of actin filaments, which further affected spindle migration. Depletion of KIFC1 leaded to aberrant expression of formin 2 and the ARP2/3 complex, and endoplasmic reticulum distribution was also disturbed. Exogenous KIFC1 mRNA supplement could rescue these defects. Taken together, as well as its roles in tubulin acetylation, our study reported a previously undescribed role of kinesin KIFC1 on the regulation of actin dynamics for spindle migration in mouse oocytes.
New Drosophila models to uncover the intrinsic and extrinsic factors that mediate the toxicity of the human prion protein
Authors: Myers Ryan R. , Sanchez-Garcia Jonatan , Leving Daniel C. , Melvin Richard G. , Fernandez-Funez Pedro
Published: February 2022

Misfolding of the prion protein (PrP) is responsible for devastating neurological disorders in humans and other mammals. An unresolved problem in the field is unraveling the mechanisms governing PrP conformational dynamics, misfolding, and the cellular mechanism leading to neurodegeneration. The variable susceptibility of mammals to prion diseases is a natural resource that can be exploited to understand the conformational dynamics of PrP. Here we present a new fly model expressing human PrP with new, robust phenotypes in brain neurons and the eye. By using comparable attP2 insertions, we demonstrated the heightened toxicity of human PrP compared to rodent PrP along with a specific interaction with the amyloid-β peptide. By using this new model, we started to uncover the intrinsic (sequence/structure) and extrinsic (interactions) factors regulating PrP toxicity. We described PERK (officially known as EIF2AK3 in humans) and activating transcription factor 4 (ATF4) as key in the cellular mechanism mediating the toxicity of human PrP and uncover a key new protective activity for 4E-BP (officially known as Thor in Drosophila and EIF4EBP2 in humans), an ATF4 transcriptional target. Lastly, mutations in human PrP (N159D, D167S, N174S) showed partial protective activity, revealing its high propensity to misfold into toxic conformations.
A genetic screen inDrosophilareveals the role of fucosylation in host susceptibility toCandidainfection
Authors: Glittenberg Marcus T. , Kounatidis Ilias , Atilano Magda , Ligoxygakis Petros
Published: February 2022

Candida infections constitute a blind spot in global public health as very few new anti-fungal drugs are being developed. Genetic surveys of host susceptibilities to such infections using mammalian models have certain disadvantages in that obtaining results is time-consuming, owing to relatively long lifespans, and these results have low statistical resolution because sample sizes are usually small. Here, we report a targeted genetic screening of 5698 RNAi lines encompassing 4135 Drosophila genes with human homologues, several of which we identify as important for host survival after Candida albicans infection. These include genes in a variety of functional classes encompassing gene expression, intracellular signalling, metabolism and enzymatic regulation. Analysis of one of the screen hits, the infection-induced α-(1,3)-fucosylase FucTA, showed that N-glycan fucosylation has several targets among proteins involved in host defence, which provides multiple avenues of investigation for the mechanistic analysis of host survival to systemic C. albicans infection.
COPD identification and grading based on deep learning of lung parenchyma and bronchial wall in chest CT images
Authors: Zhang Lin , Jiang Beibei , Wisselink Hendrik Joost , Vliegenthart Rozemarijn , Xie Xueqian
Published: February 2022

Objective

Chest CT can display the main pathogenic factors of chronic obstructive pulmonary disease (COPD), emphysema and airway wall remodeling. This study aims to establish deep convolutional neural network (CNN) models using these two imaging markers to diagnose and grade COPD.

Methods

Subjects who underwent chest CT and pulmonary function test (PFT) from one hospital (n = 373) were retrospectively included as the training cohort, and subjects from another hospital (n = 226) were used as the external test cohort. According to the PFT results, all subjects were labeled as Global Initiative for Chronic Obstructive Lung Disease (GOLD) Grade 1, 2, 3, 4 or normal. Two DenseNet-201 CNNs were trained using CT images of lung parenchyma and bronchial wall to generate two corresponding confidence levels to indicate the possibility of COPD, then combined with logistic regression analysis. Quantitative CT was used for comparison.

Results:

In the test cohort, CNN achieved an area under the curve of 0.899 (95%CI: 0.853–0.935) to determine the existence of COPD, and an accuracy of 81.7% (76.2–86.7%), which was significantly higher than the accuracy 68.1% (61.6%–74.2%) using quantitative CT method (p < 0.05). For three-way (normal, GOLD 1–2, and GOLD 3–4) and five-way (normal, GOLD 1, 2, 3, and 4) classifications, CNN reached accuracies of 77.4 and 67.9%, respectively.

Conclusion

CNN can identify emphysema and airway wall remodeling on CT images to infer lung function and determine the existence and severity of COPD. It provides an alternative way to detect COPD using the extensively available chest CT.

Advances in knowledge

CNN can identify the main pathological changes of COPD (emphysema and airway wall remodeling) based on CT images, to infer lung function and determine the existence and severity of COPD. CNN reached an area under the curve of 0.853 to determine the existence of COPD in the external test cohort. The CNN approach provides an alternative and effective way for early detection of COPD using extensively used chest CT, as an important alternative to pulmonary function test.