bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated contouring and planning pipeline for hippocampal-avoidant whole-brain radiotherapy
Authors: Feng Christine H. , Cornell Mariel , Moore Kevin L. , Karunamuni Roshan , Seibert Tyler M. 
Published: October 2020

Abstract

Background
Whole-brain radiotherapy (WBRT) remains an important treatment for over 200,000 cancer patients in the United States annually. Hippocampal-avoidant WBRT (HA-WBRT) reduces neurocognitive toxicity compared to standard WBRT, but HA-WBRT contouring and planning are more complex and time-consuming than standard WBRT. We designed and evaluated a workflow using commercially available artificial intelligence tools for automated hippocampal segmentation and treatment planning to efficiently generate clinically acceptable HA-WBRT radiotherapy plans.

Methods
We retrospectively identified 100 consecutive adult patients treated for brain metastases outside the hippocampal region. Each patient’s T1 post-contrast brain MRI was processed using NeuroQuant, an FDA-approved software that provides segmentations of brain structures in less than 8 min.
Automated hippocampal segmentations were reviewed for accuracy, then converted to files compatible with a commercial treatment planning system, where hippocampal avoidance regions and planning target volumes (PTV) were generated. Other organs-at-risk (OARs) were previously contoured per clinical routine. A RapidPlan knowledge-based planning routine was applied for a prescription of 30 Gy in 10 fractions using volumetric modulated arc therapy (VMAT) delivery. Plans were evaluated based on NRG CC001 dose-volume objectives (Brown et al. in J Clin Oncol, 2020).

Results
Of the 100 cases, 99 (99%) had acceptable automated hippocampi segmentations without manual intervention. Knowledge-based planning was applied to all cases; the median processing time was 9 min 59 s (range 6:53–13:31). All plans met per-protocol dose-volume objectives for PTV per the NRG CC001 protocol. For comparison, only 65.5% of plans on NRG CC001 met PTV goals per protocol, with 26.1% within acceptable variation. In this study, 43 plans (43%) met OAR constraints, and the remaining 57 (57%) were within acceptable variation, compared to 42.5% and 48.3% on NRG CC001, respectively. No plans in this study had unacceptable dose to OARs, compared to 0.8% of manually generated plans from NRG CC001. 8.4% of plans from NRG CC001 were not scored or unable to be evaluated.

Conclusions
An automated pipeline harnessing the efficiency of commercially available artificial intelligence tools can generate clinically acceptable VMAT HA-WBRT plans with minimal manual intervention. This process could improve clinical efficiency for a treatment established to improve patient outcomes over standard WBRT.
COVID-19: a potential driver of immune-mediated breast cancer recurrence?
Authors: Francescangeli Federica , De Angelis Maria Laura , Zeuner Ann 
Published: October 2020

Abstract
Severe coronavirus disease 2019 (COVID-19) causes a hyperactivation of immune cells, resulting in lung inflammation. Recent studies showed that COVID-19 induces the production of factors previously implicated in the reawakening of dormant breast cancer cells such as neutrophil extracellular traps (NETs). The presence of NETs and of a pro-inflammatory microenvironment may therefore promote breast cancer reactivation, increasing the risk of pulmonary metastasis. Further studies will be required to confirm the link between COVID-19 and cancer recurrence. However, an increased awareness on the potential risks for breast cancer patients with COVID-19 may lead to improved treatment strategies to prevent metastatic relapse.
New insights into prediction of weak π–π complex association through proton-nuclear magnetic resonance analysis
Authors: Lin Chenyu , Skufca Joseph , Partch Richard E. 
Published: October 2020

Abstract
For analysis of weak π–π complexes proton-nuclear magnetic resonance (proton-NMR) simultaneously provides information of stacking configurations and association constants $$\left( K \right)$$

K

However, an apparent issue for this approach is inconsistent/impossible constant estimation which often leads to unreasonable interpretation for π–π complexation. Whether or not this proton-dependent constant variation could be attributed to simple experimental uncertainties or to more sophisticated additional unspecific shielding effects (AUS effects) was addressed by means of hypothesis tests using a robust bootstrap technique in this report. Our analysis shows the significance of AUS effects on such variation in constant estimation. A following study using numeric simulation further reveals the variation patterns induced by AUS effects and concludes that the largest $$K$$
K
among the obtained $$K$$
K
estimates of a complex is considered as the best estimate of $$K$$
K
due to minimum deviation from the true value of K and the multiple $$K$$
K
estimates of a π–π complex could provide preferable inferences for complex geometries.
No evidence for sylvatic cycles of chikungunya, dengue and Zika viruses in African green monkeys (Chlorocebus aethiops sabaeus) on St. Kitts, West Indies
Authors: Valentine Matthew John , Ciraola Brenda , Aliota Matthew Thomas , Vandenplas Michel , Marchi Silvia , Tenebray Bernard , Leparc-Goffart Isabelle , Gallagher Christa Ann , Beierschmitt Amy , Corey Tatiana , Dore Kerry McAuliffe , de Lamballerie Xavier , Wang Chengming , Murdock Courtney Cuin , Kelly Patrick John 
Published: October 2020

AbstractBackgroundDengue, chikungunya and Zika viruses (DENV, CHIKV and ZIKV) are transmitted in sylvatic transmission cycles between non-human primates and forest (sylvan) mosquitoes in Africa and Asia. It remains unclear if sylvatic cycles exist or could establish themselves elsewhere and contribute to the epidemiology of these diseases. The Caribbean island of St. Kitts has a large African green monkey (AGM) (Chlorocebus aethiops sabaeus) population and is therefore ideally suited to investigate sylvatic cycles.MethodsWe tested 858 AGM sera by ELISA and PRNT for virus-specific antibodies and collected and identified 9704 potential arbovirus vector mosquitoes. Mosquitoes were homogenized in 513 pools for testing by viral isolation in cell culture and by multiplex RT-qPCR after RNA extraction to detect the presence of DENV, CHIKV and ZIKVs. DNA was extracted from 122 visibly blood-fed individual mosquitoes and a polymorphic region of the hydroxymethylbilane synthase gene (HMBS) was amplified by PCR to determine if mosquitoes had fed on AGMs or humans.ResultsAll of the AGMs were negative for DENV, CHIKV or ZIKV antibodies. However, one AGM did have evidence of an undifferentiatedFlavivirusinfection. Similarly, DENV, CHIKV and ZIKV were not detected in any of the mosquito pools by PCR or culture. AGMs were not the source of any of the mosquito blood meals.ConclusionSylvatic cycles involving AGMs and DENV, CHIKV and ZIKV do not currently exist on St. Kitts.
Stool and sputum microbiome during quinolone prophylaxis of spontaneous bacterial peritonitis: an exploratory study
Authors: Mücke Marcus M. , Rüschenbaum Sabrina , Mayer Amelie , Mücke Victoria T. , Schwarzkopf Katharina M. , Zeuzem Stefan , Kehrmann Jan , Scholtysik René , Lange Christian M. 
Published: October 2020

AbstractIntroductionQuinolone prophylaxis is recommended for patients with advanced cirrhosis at high risk of spontaneous bacterial peritonitis (SBP) or with prior SBP. Yet, the impact of long-term antibiotic prophylaxis on the microbiome of these patients is poorly characterized.MethodsPatients with liver cirrhosis receiving long-term quinolone prophylaxis to prevent SBP were prospectively included and sputum and stool samples were obtained at baseline, 1, 4 and 12 weeks thereafter. Both bacterial DNA and RNA were assessed with 16S rRNA sequencing. Relative abundance, alpha and beta diversity were calculated and correlated with clinical outcome.ResultsOverall, 35 stool and 19 sputum samples were obtained from 11 patients. Two patients died (day 9 and 12) all others were followed for 180 days. Reduction of Shannon diversity and bacterial richness was insignificant after initiation of quinolone prophylaxis (p > 0.05). Gut microbiota were significantly different between patients (p < 0.001) but non-significantly altered between the different time points before and after initiation of antibiotic prophylaxis (p > 0.05). A high relative abundance ofEnterobacteriaceae> 20% during quinolone prophylaxis was found in three patients. Specific clinical scenarios (development of secondary infections during antibiotic prophylaxis or the detection of multidrug-resistantEnterobacteriaceae) characterized these patients. Sputum microbiota were not significantly altered in individuals during prophylaxis.ConclusionThe present exploratory study with small sample size showed that inter-individual differences in diversity of gut microbiota were high at baseline, yet quinolone prophylaxis had only a moderate impact. High relative abundances ofEnterobacteriaceaeduring follow-up might indicate failure of or non-adherence to quinolone prophylaxis. However, our results may not be clinically significant given the limitations of the study and therefore future studies are needed to further investigate this phenomenon.
Performance characteristics of a quantitative PCR assay on repository stool specimens and smeared filter-paper cards
Authors: Tisdale Michele D. , Mitra Indrani , McCoy Andrea J. , Simons Mark P. , Reynolds Nathanael D. , Swierczewski Brett E. , Liu Jie , Houpt Eric R. , Fraser Jamie A. , Riddle Mark S. , Tribble David R. , Lalani Tahaniyat 
Published: October 2020

Abstract

Objective
Stool repositories are a valuable resource for retrospective analyses including quantitative PCR assays to distinguish between asymptomatic shedding and clinical disease. The suitability of archival specimens for this purpose is unclear and requires assessment. We conducted a pilot study to evaluate pathogen detection by TaqMan Array Card (TAC) in travelers’ diarrhea (TD) stool specimens stored for 1–13 years, as well as the impact of transporting specimens on Whatman FTA Elute cards (FTA Cards) on detection.

Results
The positive percent agreement (PPA) for TAC on stool vs. microbiologic testing was lower than our a priori PPA estimate of 80% for most pathogens: Shigella spp. (100% [95%CI 69–100%]), enterotoxigenic E coli (ETEC) (63% [95%CI 49–75%]), Campylobacter spp. (66% [95%CI 43–85%]) and Norovirus (37% [95%CI 16–61%]). Use of the FTA card resulted in a further reduction of PPA. Our findings suggest that archival specimens may lead to insensitive detection on quantitative PCR assays due to degradation of nucleic acid with prolonged storage, although our limited sample size precluded us from evaluating the impact of storage duration on nucleic acid yield. Additional studies are needed to understand the impact of storage duration on quantitative PCR data.
The impact of different suturing techniques for abdominal fascia closure on the Interleukin-6 expressions in Rattus norvegicus
Authors: Prima Heryu , Sofii Imam , Fauzi Aditya Rifqi , Dachlan Ishandono , Gunadi  
Published: October 2020

Abstract

Objective
Incisional hernia is a frequent complication of midline laparotomy. The suturing technique is an important determinant of the risk of developing an incisional hernia. Moreover, IL-6 has crucial roles in the wound-healing process. We aimed to compare the large stitch vs. small stitch technique for abdominal fascial closure on IL-6 expressions in rats.

Results
Twenty rats were used. The small stitch group received small tissue bites of 5 mm and the large stitch group received large bites of 10 mm. The incisions of fascia were closed by running sutures. Animals were euthanized on days 4 and 7. Histological sections of the tissue-embedded sutures were analyzed for IL-6 expressions. Two-way ANOVA showed that rats in the small stitch group had similar IL-6 expressions on days 4 and 7 to those in the large stitch group (p = 0.36). In conclusion, the IL-6 expressions are similar between the small and the large stitch groups, implying that different suturing techniques might not have an impact on the incisional hernia occurrence.
Gray matter covariations and core symptoms of autism: the EU-AIMS Longitudinal European Autism Project
Authors:   the EU-AIMS LEAP group, Mei Ting , Llera Alberto , Floris Dorothea L. , Forde Natalie J. , Tillmann Julian , Durston Sarah , Moessnang Carolin , Banaschewski Tobias , Holt Rosemary J. , Baron-Cohen Simon , Rausch Annika , Loth Eva , Dell’Acqua Flavio , Charman Tony , Murphy Declan G. M. , Ecker Christine , Beckmann Christian F. , Buitelaar Jan K. 
Published: October 2020

AbstractBackgroundVoxel-based morphometry (VBM) studies in autism spectrum disorder (autism) have yielded diverging results. This might partly be attributed to structural alterations being associating with the combined influence of several regions rather than with a single region. Further, these structural covariation differences may relate to continuous measures of autism rather than with categorical case–control contrasts. The current study aimed to identify structural covariation alterations in autism, and assessed canonical correlations between brain covariation patterns and core autism symptoms.MethodsWe studied 347 individuals with autism and 252 typically developing individuals, aged between 6 and 30 years, who have been deeply phenotyped in the Longitudinal European Autism Project. All participants’ VBM maps were decomposed into spatially independent components using independent component analysis. A generalized linear model (GLM) was used to examine case–control differences. Next, canonical correlation analysis (CCA) was performed to separately explore the integrated effects between all the brain sources of gray matter variation and two sets of core autism symptoms.ResultsGLM analyses showed significant case–control differences for two independent components. The first component was primarily associated with decreased density of bilateral insula, inferior frontal gyrus, orbitofrontal cortex, and increased density of caudate nucleus in the autism group relative to typically developing individuals. The second component was related to decreased densities of the bilateral amygdala, hippocampus, and parahippocampal gyrus in the autism group relative to typically developing individuals. The CCA results showed significant correlations between components that involved variation of thalamus, putamen, precentral gyrus, frontal, parietal, and occipital lobes, and the cerebellum, and repetitive, rigid and stereotyped behaviors and abnormal sensory behaviors in autism individuals.LimitationsOnly 55.9% of the participants with autism had complete questionnaire data on continuous parent-reported symptom measures.ConclusionsCovaried areas associated with autism diagnosis and/or symptoms are scattered across the whole brain and include the limbic system, basal ganglia, thalamus, cerebellum, precentral gyrus, and parts of the frontal, parietal, and occipital lobes. Some of these areas potentially subserve social-communicative behavior, whereas others may underpin sensory processing and integration, and motor behavior.
Differentially altered social dominance- and cooperative-like behaviors in Shank2- and Shank3-mutant mice
Authors: Han Kyung Ah , Yoon Taek Han , Shin Jungsu , Um Ji Won , Ko Jaewon 
Published: October 2020

Abstract
Background
Recent progress in genomics has contributed to the identification of a large number of autism spectrum disorder (ASD) risk genes, many of which encode synaptic proteins. Our understanding of ASDs has advanced rapidly, partly owing to the development of numerous animal models. Extensive characterizations using a variety of behavioral batteries that analyze social behaviors have shown that a subset of engineered mice that model mutations in genes encoding Shanks, a family of excitatory postsynaptic scaffolding proteins, exhibit autism-like behaviors. Although these behavioral assays have been useful in identifying deficits in simple social behaviors, alterations in complex social behaviors remain largely untested.

Methods
Two syndromic ASD mouse models—Shank2 constitutive knockout [KO] mice and Shank3 constitutive KO mice—were examined for alterations in social dominance and social cooperative behaviors using tube tests and automated cooperation tests. Upon naïve and salient behavioral experience, expression levels of c-Fos were analyzed as a proxy for neural activity across diverse brain areas, including the medial prefrontal cortex (mPFC) and a number of subcortical structures.

Findings
As previously reported, Shank2 KO mice showed deficits in sociability, with intact social recognition memory, whereas Shank3 KO mice displayed no overt phenotypes. Strikingly, the two Shank KO mouse models exhibited diametrically opposed alterations in social dominance and cooperative behaviors. After a specific social behavioral experience, Shank mutant mice exhibited distinct changes in number of c-Fos+ neurons in the number of cortical and subcortical brain regions.

Conclusions
Our results underscore the heterogeneity of social behavioral alterations in different ASD mouse models and highlight the utility of testing complex social behaviors in validating neurodevelopmental and neuropsychiatric disorder models. In addition, neural activities at distinct brain regions are likely collectively involved in eliciting complex social behaviors, which are differentially altered in ASD mouse models.
Subspecialized radiological reporting reduces radiology report turnaround time
Authors: Zabel Andreas Otto Josef , Leschka Sebastian , Wildermuth Simon , Hodler Juerg , Dietrich Tobias Johannes 
Published: October 2020

Abstract

Objectives
The objective of this study was to compare the radiology report turnaround time (RTAT) between decentralized/modality-based and centralized/subspecialized radiological reporting at a multi-center radiology enterprise.

Methods
RTAT values for MRI, CT, and conventional radiography were compared between decentralized/modality-based (04 September 2017–22 December 2017) and centralized/subspecialized radiology (03 September 2018–21 December 2018) reporting grouped into three subspecializations (body radiology, musculoskeletal radiology, and neuroradiology) at eleven sites of a multi-center radiology enterprise. For the objective of this investigation, hospitals were defined as major and minor hospitals. The Mann-Whitney U test served for statistical analyses.

Results
Change of reporting system from decentralized/modality-based to centralized/subspecialized radiology resulted overall in a significant decrease of the RTAT: from 82 to 77 min for the first signature (p < 0.001), and 119 to 107 min and 295 to 238 min for the second signature (p < 0.001). Subgroup analyses demonstrate a significant decrease of the RTAT for MRI reports (e.g., second signature RTAT, 1051 to 401 min; p < 0.001) and conventional radiographs (e. g., second signature RTAT, 278 to 171 min; p < 0.001). The RTAT at major hospitals decreased from 288 to 245 min (second signature; p < 0.001) while the corresponding RTAT of minor hospitals decreased more remarkably, from 300 to 198 min (p < 0.001). However, the results were heterogenous; in some analyses, the RTAT even increased. The effect size analyses represent small effects.

Conclusions
Change of reporting system from decentralized/modality-based to centralized/subspecialized radiology was associated with a significant decreased RTAT. Specifically, the RTAT for MRI reports and conventional radiographs was significantly reduced. A pronounced RTAT decrease was observed at minor hospitals.
Acquired hemophilia A and plasma cell neoplasms: a case report and review of the literature
Authors: Jalowiec Katarzyna A. , Andres Martin , Taleghani Behrouz Mansouri , Musa Albulena , Dickenmann Martina , Angelillo-Scherrer Anne , Rovó Alicia , Kremer Hovinga Johanna A. 
Published: October 2020

AbstractBackgroundAcquired hemophilia A is a rare autoimmune disease with clinically often significant bleeding diathesis resulting from circulating autoantibodies inhibiting coagulation factor VIII. Half of acquired hemophilia A cases are associated with an underlying disorder, such as autoimmune diseases, cancer, or use of certain drugs, or occur during pregnancy and in the postpartum period. In the other half, no underlying cause is identified. An association of acquired hemophilia A with plasma cell neoplasm seems to be extremely rare.Case presentationWe describe a case of a 77-year-old Swiss Caucasian man who was diagnosed with acquired hemophilia A and smoldering multiple myeloma as an underlying cause. Acquired hemophilia A was treated with prednisolone, cyclophosphamide, and immunoadsorption. Extensive workup revealed a plasma cell neoplasm as the only disorder associated with or underlying the acquired hemophilia A. For long-term control of acquired hemophilia A, we considered treatment of the plasma cell neoplasm necessary, and a VRD (bortezomib, lenalidomide, and dexamethasone) regimen was initiated. Due to multiple complications, VRD was reduced to VRD-lite after two cycles. After nine cycles of induction therapy and five cycles of consolidation therapy, the patient is in complete remission of his acquired hemophilia A and very good partial remission of the plasma cell neoplasm. We conducted a literature review to identify additional cases of this rare association and identified 15 other cases. Case descriptions, including the sequence of occurrence of acquired hemophilia A and plasma cell neoplasm , treatment, evolution, and outcome are presented.Discussion and conclusionsOur case, together with 15 other cases described in the literature, underscore the possibility of plasma cell neoplasm as an underlying cause of acquired hemophilia A. Physicians should consider including protein electrophoresis, immunofixation, and analysis of free light chains in laboratory diagnostics when treating a patient with acquired hemophilia A. The occurrence of excessive and unexplained bleeding in patients diagnosed with plasma cell neoplasm should raise suspicion of secondary acquired hemophilia A and trigger the request for coagulation tests, particularly in patients treated with immunomodulatory drugs such as thalidomide or lenalidomide. Additionally, early intervention with immunoadsorption can be lifesaving in cases with high-titer factor VIII inhibitors, especially when surgical interventions are necessary.