bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary fibrosis in a dog as a sequela of infection with Severe Acute Respiratory Syndrome Coronavirus 2? A case report
Authors: Colitti Barbara , Manassero Luca , Colombino Elena , Ferraris Erica Ilaria , Caccamo Roberta , Bertolotti Luigi , Bortolami Alessio , Bonfante Francesco , Papa Valentina , Cenacchi Giovanna , Calabrese Fiorella , Bozzetta Elena , Varello Katia , Capucchio Maria Teresa , Rosati Sergio 
Published: March 2022

Abstract
Background
Interstitial lung disease is a heterogeneous group of conditions characterized by severe radiographic changes and clinicopathological findings. However, in the vast majority of cases, the cause remains unknown.

Case description
In the present study, we reported the clinical case of a 3 years old female Bull Terrier presented in October 2020 to the Advanced Diagnostic Imaging Department of the Turin Veterinary Teaching Hospital with a progressive pulmonary illness characterized by dyspnea, exercise intolerance, and a diffuse and severe pulmonary interstitial pattern at imaging investigations.
Considering the clinical findings, the dog was included in a serological survey for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in companion animals, showing positive results. Due to the further clinical worsening, the owners opted for euthanasia. At necroscopy, dog showed severe and chronic bronchopneumonia compatible with a Canine Idiopathic Pulmonary Fibrosis and with serological features linked to a SARS-CoV-2 infection.

Conclusions
The comparison of these lesions with those reported in humans affected by Coronavirus Disease 2019 (COVID-19) supports the hypothesis that these findings may be attributable to the post-acute sequelae of SARS-CoV-2 infection in a dog with breed predisposition to Canine Idiopathic Pulmonary Fibrosis (CIPF), although direct evidence of SARS-CoV-2 by molecular or antigenic approaches remained unsolved.
Cerebrospinal fluid production by the choroid plexus: a century of barrier research revisited
Authors: MacAulay Nanna , Keep Richard F. , Zeuthen Thomas 
Published: March 2022

AbstractCerebrospinal fluid (CSF) envelops the brain and fills the central ventricles. This fluid is continuously replenished by net fluid extraction from the vasculature by the secretory action of the choroid plexus epithelium residing in each of the four ventricles. We have known about these processes for more than a century, and yet the molecular mechanisms supporting this fluid secretion remain unresolved. The choroid plexus epithelium secretes its fluid in the absence of a trans-epithelial osmotic gradient, and, in addition, has an inherent ability to secrete CSF against an osmotic gradient. This paradoxical feature is shared with other ‘leaky’ epithelia. The assumptions underlying the classical standing gradient hypothesis await experimental support and appear to not suffice as an explanation of CSF secretion. Here, we suggest that the elusive local hyperosmotic compartment resides within the membrane transport proteins themselves. In this manner, the battery of plasma membrane transporters expressed in choroid plexus are proposed to sustain the choroidal CSF secretion independently of the prevailing bulk osmotic gradient.
Circulatory metabolites trigger ex vivo arterial endothelial cell dysfunction in population chronically exposed to diesel exhaust
Authors: Cheng Wenting , Pang Huanhuan , Campen Matthew J. , Zhang Jianzhong , Li Yanting , Gao Jinling , Ren Dunqiang , Ji Xiaoya , Rothman Nathaniel , Lan Qing , Zheng Yuxin , Leng Shuguang , Hu Zeping , Tang Jinglong 
Published: March 2022

Abstract
Background
Chronic exposure to diesel exhaust has a causal link to cardiovascular diseases in various environmental and occupational settings. Arterial endothelial cell function plays an important role in ensuring proper maintenance of cardiovascular homeostasis and the endothelial cell dysfunction by circulatory inflammation is a hallmark in cardiovascular diseases. Acute exposure to diesel exhaust in controlled exposure studies leads to artery endothelial cells dysfunction in previous study, however the effect of chronic exposure remains unknown.

Results
We applied an ex vivo endothelial biosensor assay for serum samples from 133 diesel engine testers (DETs) and 126 non-DETs with the aim of identifying evidence of increased risk for cardiovascular diseases. Environmental monitoring suggested that DETs were exposed to high levels of diesel exhaust aerosol (282.3 μg/m3 PM2.5 and 135.2 μg/m3 elemental carbon). Surprisingly, chronic diesel exhaust exposure was associated with a pro-inflammatory phenotype in the ex vivo endothelial cell model, in a dose-dependent manner with CCL5 and VCAM as most affected genes. This dysfunction was not mediated by reduction in circulatory pro-inflammatory factors but significantly associated with a reduction in circulatory metabolites cGMP and an increase in primary DNA damage in leucocyte in a dose-dependent manner, which also explained a large magnitude of association between diesel exhaust exposure and ex vivo endothelial biosensor response. Exogenous cGMP addition experiment further confirmed the induction of ex vivo biosensor gene expressions in endothelial cells treated with physiologically relevant levels of metabolites cGMP.

Conclusion
Serum-borne bioactivity caused the arterial endothelial cell dysfunction may attribute to the circulatory metabolites based on the ex vivo biosensor assay. The reduced cGMP and increased polycyclic aromatic hydrocarbons metabolites-induced cyto/geno-toxic play important role in the endothelial cell dysfunction of workers chronic exposure to diesel exhaust.
Space-efficient representation of genomic k-mer count tables
Authors: Shibuya Yoshihiro , Belazzougui Djamal , Kucherov Gregory 
Published: March 2022

Abstract
Motivation
k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k-mers and counts, easily reaching tens of GB. Furthermore, such tables do not support efficient random-access queries in general.

Results
In this work, we design an efficient representation of k-mer count tables supporting fast random-access queries. We propose to apply Compressed Static Functions (CSFs), with space proportional to the empirical zero-order entropy of the counts. For very skewed distributions, like those of k-mer counts in whole genomes, the only currently available implementation of CSFs does not provide a compact enough representation. By adding a Bloom filter to a CSF we obtain a Bloom-enhanced CSF (BCSF) effectively overcoming this limitation. Furthermore, by combining BCSFs with minimizer-based bucketing of k-mers, we build even smaller representations breaking the empirical entropy lower bound, for large enough k. We also extend these representations to the approximate case, gaining additional space. We experimentally validate these techniques on k-mer count tables of whole genomes (E. Coli and C. Elegans) and unassembled reads, as well as on k-mer document frequency tables for 29 E. Coli genomes. In the case of exact counts, our representation takes about a half of the space of the empirical entropy, for large enough k’s.
Strategies for molecular authentication of herbal products: from experimental design to data analysis
Authors: Wu Hoi-Yan , Shaw Pang-Chui 
Published: March 2022

AbstractMolecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.
Surfaceome analyses uncover CD98hc as an antibody drug-conjugate target in triple negative breast cancer
Authors: Montero Juan Carlos , Calvo-Jiménez Elisa , del Carmen Sofía , Abad Mar , Ocaña Alberto , Pandiella Atanasio 
Published: March 2022

Abstract
Background
Despite the incorporation of novel therapeutics, advanced triple negative breast cancer (TNBC) still represents a relevant clinical problem. Considering this, as well as the clinical efficacy of antibody-drug conjugates (ADCs), we aimed at identifying novel ADC targets that could be used to treat TNBC.

Methods
Transcriptomic analyses were performed on TNBC and normal samples from three different studies. Plasma membrane proteins of three cell lines representative of the TNBC subtype were identified by cell surface biotinylation or plasma membrane isolation, followed by analyses of cell surface proteins using the Surfaceome online tool. Immunofluorescence and western studies were used to characterize the action of a CD98hc-directed ADC, which was prepared by in house coupling of emtansine to an antibody that recognized the ectodomain of CD98hc. Xenografted TNBC cells were used to analyze the antitumoral properties of the anti-CD98hc ADC.

Results
Comparative genomic studies between normal breast and TNBC tissues, together with proteomic and bioinformatic analyses resulted in the elaboration of a catalog of potential ADC targets. One of them, the CD98hc transmembrane protein, was validated as an ADC target. An antibody recognizing the ectodomain of CD98hc efficiently internalized and reached the lysosomal compartment. An emtansine-based ADC derived from such antibody was prepared and showed antitumoral properties in TNBC in vitro and in vivo models. Mechanistically, the anti-CD98hc ADC blocked cell cycle progression, that was followed by cell death caused by mitotic catastrophe.

Conclusions
This work describes a list of potential ADC targets in TNBC and validates one of them, the transmembrane protein CD98hc. The studies presented here also demonstrate the robustness of the multiomic approach herewith described to identify novel potential ADC targets.
Validation of fatty liver index as a marker for metabolic dysfunction-associated fatty liver disease
Authors: Han A Lum 
Published: March 2022

Abstract
Aims
Metabolic dysfunction-associated fatty liver disease (MAFLD) is a new nomenclature for nonalcoholic fatty liver. Along with obesity, fatty liver associated with metabolic dysfunction is increasing and has become a serious socioeconomic problem. Non-invasive testing for the confirmation of MAFLD, including the fatty liver index (FLI), can be used as an alternative method for diagnosing steatosis when imaging modalities are not available. To date, few studies have examined the effectiveness and validity of FLI for diagnosing MAFLD. Therefore, this study analyzed the effectiveness and validity of FLI for diagnosing MAFLD.

Methods
Medical records of men and women aged ≥ 19 years who underwent abdominal computed tomography (CT) examination at our facility between March 2012 and October 2019 were retrospectively reviewed. A comparative analysis between non-continuous variables was performed using the chi-squared test. The area under receiver operating characteristic (AUROC) curve was used to verify the effectiveness of FLI as a predictive index for MAFLD.

Results
Analysis of the association between MAFLD and abdominal CT revealed that the sensitivity and specificity of FLI for diagnosing MAFLD were 0.712 and 0.713, respectively. The AUROC of FLI for predicting MAFLD was 0.776.

Conclusions
Our study verified the accuracy of FLI for predicting MAFLD using CT. The FLI can be used as a simple and cost-effective tool for screening MAFLD in clinical settings.
Chromosome length genome assembly of the redbanded stink bug, Piezodorus guildinii (Westwood)
Authors: Saha Surya , Allen K. Clint , Mueller Lukas A. , Reddy Gadi V. P. , Perera Omaththage P. 
Published: March 2022

Abstract
Objective
The redbanded stink bug (RBSB), Piezodorus guildinii (Hemiptera: Pentatomidae), is native to the Caribbean Basin and is currently considered an invasive pest in Florida, Louisiana, Mississippi, and Texas in the southern United States. Although RBSB is an economically important invasive pest in the USA, relatively few studies have been conducted to understand molecular mechanisms, population genetic structure, and the genetic basis of resistance to insecticides. The objective of this work was to obtain a high-quality genome assembly to develop genomic resources to conduct population genetic, genomic, and physiological studies of the RBSB.

Results
The genome of RBSB was sequenced with Pacific Biosciences technology followed by two rounds of scaffolding using Chicago libraries and HiC proximity ligation to obtain a high-quality assembly. The genome assembly contained 800 scaffolds larger than 1 kbp and the N50 was 170.84 Mbp. The largest scaffold was 222.22 Mbp and 90% of the genome was included in the 7 scaffolds larger than 118 Mbp. The number of megabase scaffolds also matched the number of chromosomes in this insect. The genome sequence will facilitate the development of resources to conduct studies on genetics, transcriptomics, and physiology of RBSB.
Visual programming for accessible interactive musculoskeletal models
Authors: Manczurowsky Julia , Badadhe Mansi , Hasson Christopher J. 
Published: March 2022

Abstract
Objective
Musculoskeletal modeling and simulation are powerful research and education tools in engineering, neuroscience, and rehabilitation. Interactive musculoskeletal models (IMMs) can be controlled by muscle activity recorded with electromyography (EMG). IMMs are typically coded using textual programming languages that present barriers to understanding for non-experts. The goal of this project was to use a visual programming language (Simulink) to create and test an IMM that is accessible to non-specialists for research and educational purposes.

Results
The developed IMM allows users to practice a goal-directed task with different control modes (keyboard, mouse, and EMG) and actuator types (muscle model, force generator, and torque generator). Example data were collected using both keyboard and EMG control. One male participant in his early 40’s performed a goal-directed task for four sequential trials using each control mode. For EMG control, the participant used a low-cost EMG system with consumer-grade EMG sensors and an Arduino microprocessor. The participant successfully performed the task with both control modes, but the inability to grade muscle model excitation and co-activate antagonist muscles limited performance with keyboard control. The IMM developed for this project serves as a foundation that can be further tailored to specific research and education needs.
Statistical inference for ordinal predictors in generalized additive models with application to Bronchopulmonary Dysplasia
Authors: Gertheiss Jan , Scheipl Fabian , Lauer Tina , Ehrhardt Harald 
Published: March 2022

AbstractObjectiveDiscrete but ordered covariates are quite common in applied statistics, and some regularized fitting procedures have been proposed for proper handling of ordinal predictors in statistical models. Motivated by a study from neonatal medicine on Bronchopulmonary Dysplasia (BPD), we show how quadratic penalties on adjacent dummy coefficients of ordinal factors proposed in the literature can be incorporated in the framework of generalized additive models, making tools for statistical inference developed there available for ordinal predictors as well.ResultsThe approach presented allows to exploit the scale level of ordinally scaled factors in a sound statistical framework. Furthermore, several ordinal factors can be considered jointly without the need to collapse levels even if the number of observations per level is small. By doing so, results obtained earlier on the BPD data analyzed could be confirmed.
Hypereosinophilic syndrome presenting as coagulopathy
Authors: Aukstuolis Kestutis , Cooper Jocelyn J. , Altman Katherine , Lang Anna , Ayars Andrew G. 
Published: March 2022

Abstract
Background
Hypereosinophilic syndrome (HES) is an extremely uncommon group of disorders. It rarely presents with coagulopathy without cardiac involvement.

Case presentation
A 33-year-old previously healthy male with no history of atopic disease presented with abdominal pain, hematochezia, peripheral eosinophilia as high as 10,000 eos/µL, right and left portal vein, mesenteric, and splenic vein thrombi with ischemic colitis resulting in hemicolectomy and small bowel resection. Despite an extensive workup for primary and secondary etiologies of hypereosinophilia by hematology/oncology, infectious disease, rheumatology and allergy/immunology, no other clear causes were identified, and the patient was diagnosed with idiopathic HES. His eosinophilia was successfully treated with high-dose oral corticosteroids (OCS) and subsequently transitioned to anti-IL-5-receptor therapy with benralizumab. He has continued this treatment for over a year with no recurrence of eosinophilia or thrombosis while on benralizumab.

Conclusion
In patients with an unexplained coagulopathy and eosinophilia, eosinophilic disorders such as HES should be considered. Corticosteroid-sparing agents, such as benralizumab show promise for successfully treating these patients.
Performance comparison of ultrasonography and magnetic resonance imaging in their diagnostic accuracy of placenta accreta spectrum disorders: a systematic review and meta-analysis
Authors: Hong Shibin , Le Yiping , Lio Ka U. , Zhang Ting , Zhang Yu , Zhang Ning 
Published: March 2022

AbstractObjectivesAccurate prenatal diagnosis of placenta accrete spectrum disorder (PAS) remains a challenge, and the reported diagnostic value of ultrasonography (US) and magnetic resonance imaging (MRI) varies widely. This study aims to systematically evaluate the diagnostic accuracy of US as compared with MRI in the detection of PAS within the identical patient population.MethodsMedline, EMBASE, Google scholar and Cochrane library were searched. Pooled sensitivity, specificity, diagnostic odds ratio (DOR) and the area under the summary receiver operating characteristic (SROC) curve were calculated. Subgroup analysis was also performed to elucidate the heterogeneity of results.ResultsA total of 18 articles comprising 861 pregnancies were included in the study. The overall diagnostic accuracy of US for identification of PAS was as follows: sensitivity [0.90 (0.86–0.93)], specificity [0.83 (0.79–0.86)], DOR [39.5 (19.6–79.7)]. The overall diagnostic accuracy of MRI for identification of PAS was as follows: sensitivity [0.89 (0.85-0.92)], specificity [0.87 (0.83–0.89)], DOR [37.4 (17.0–82.3)]. The pooled sensitivity (p = 0.808) and specificity (p = 0.413) between US and MRI are not significantly different. SROC analysis revealed that there was no statistical difference (p = 0.552) in US and MRI for the overall predictive accuracy of PAS. Furthermore, in the subgroup analysis of between retrospective and prospective studies, between earlier and most recent studies, there was no statistical difference (p > 0.05) in diagnostic accuracy of US and MRI for the detection of PAS.ConclusionsBoth ultrasonography (US) and magnetic resonance imaging (MRI) showed comparable accuracy in the prenatal diagnosis of placenta accrete spectrum disorder (PAS). Routine employment of MRI with relatively high expense in the prenatal identification of PAS should not be recommended.
Differential diagnosis of localized pneumonic-type lung adenocarcinoma and pulmonary inflammatory lesion
Authors: Li Qi , Fan Xiao , Huo Ji-wen , Luo Tian-you , Huang Xing-tao , Gong Jun-wei 
Published: March 2022

Abstract
Background
In clinical practice, a number of delayed diagnoses of localized pneumonic-type lung adenocarcinoma (L-PLADC) mimicking pneumonia have been identified due to the lack of knowledge regarding the radiological findings associated with this condition. Here, we defined L-PLADC as a special type of lung adenocarcinoma that presents as a focal consolidation involving < 50% of the area of a lobe and aimed to investigate the differential clinical and imaging features between L-PLADC and localized pulmonary inflammatory lesion (L-PIL).

Results
The data of 120 patients with L-PLADC and 125 patients with L-PIL who underwent contrast-enhanced chest computed tomography (CT) scan were retrospectively analyzed. For clinical characteristics, older age, women, nonsmokers, and no symptom were more common in L-PLADC (all p < 0.001). With regard to CT features, air bronchogram, irregular air bronchogram, ground-glass opacity (GGO) component, and pleural retraction were more frequently observed in L-PLADC, while necrosis, satellite lesions, halo sign, bronchial wall thickening, interlobular septa thickening, pleural attachment, and pleural thickening were more commonly seen in L-PIL (all p < 0.001). Multivariate analysis showed age ≥ 58 years, female sex, GGO component, irregular air bronchogram, pleural retraction, and the absence of necrosis and pleural attachment were the most effective variations associated with L-PLADC with an AUC of 0.979. Furthermore, an external validation cohort containing 62 patients obtained an AUC of 0.929.

Conclusions
L-PLADC and L-PIL have different clinical and imaging characteristics. An adequate understanding of these differential features can contribute to the early diagnosis of L-PLADC and the subsequent therapeutic strategy.