bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clear cell sarcoma of soft tissue with plasmacytoid morphology: A rare case report
Authors: Han Xu , Li Qingchang , Wang En-Hua , Liu Nan 
Published: November 2022

Rationale:
Clear cell sarcoma of soft tissue (CCSST) is a rare malignant tumor that occurs in the extremities of young adults. CCSST has been documented to have atypical histopathological features, such as epidermotropism or myxoid differentiation, which may set pitfalls in the differential diagnosis. We report a case of CCSST with plasmacytoid morphology which has never been described.

Patient concerns:
A 15-year-old male, presented with a 5-cm mass in his left inguinal area.

Diagnosis:
Positron emission tomography-computed tomography examination showed nodules in the left groin and the lung, the latter was considered metastasis. A core needle biopsy with the diagnosis of CCSST with plasmacytoid morphology was made according to histology, immunostaining, and molecular analysis.

Interventions:
The patient received chemotherapy of doxorubicin and ifosfamide.

Outcomes:
The patient failed to respond to the standard chemotherapy and deceased twelve months after diagnosis.

Lessons:
This special case of CCSST with plasmacytoid features demonstrated a morphological variation never been documented and may easily lead to misdiagnosis. For such cases, molecular analysis is essential to provide solid evidence for accurate diagnosis.
The tilts, twists, and turns of torticollis
Authors: Gross Preston W. , Chipman Danielle E. , Doyle Shevaun M. 
Published: November 2022

Purpose of review
The purpose of this review is to outline the most recent understanding of torticollis in the pediatric population.

Recent findings
It is important to diagnose the underlying condition of torticollis early in childhood, as some conditions that cause torticollis may result in major developmental delays in early motor milestones. Recent studies have highlighted that many of the rarer causes of torticollis are often misdiagnosed as congenital muscular torticollis, suggesting that physicians should pay close attention to the results of clinical and radiographic examinations when patients present with torticollis.

Summary
Congenital muscular torticollis is the most common cause of torticollis. Other, less common causes of torticollis include vertebral abnormalities, ocular torticollis, gastrointestinal disorders, soft tissue infections of the neck, posterior fossa tumors, and benign paroxysmal torticollis. Although rare, these differential diagnoses should be considered during a clinical work-up for a patient who presents with torticollis.
Changes in Substance Use and Sexual Behaviors After a Sexually Transmitted Infection Diagnosis Among a Cohort of Men Who Have Sex With Men in Los Angeles, CA
Authors: Javanbakht Marjan , Miller Amanda P. , Moran Alexander , Ragsdale Amy , Bolan Robert , Shoptaw Steve , Gorbach Pamina M. 
Published: November 2022

Despite declines in substance use and sexual behaviors after a sexually transmitted infection, reinfections were high suggesting that men who have sex with men with sexually transmitted infections occupy sexual networks with high transmission probabilities and prevention efforts should consider sexual network characteristics.

Background
Sexually transmitted infections (STIs), STI reinfection, human immunodeficiency virus (HIV) acquisition, and changes in behaviors after an STI were examined in a cohort of men who have sex with men (MSM) in Los Angeles, CA.

Methods
Data from a longitudinal study of MSM enrolled from 2014 with at least 1 follow-up visit through March 2020 were analyzed (n = 447; 1854 visits). Study visits every 6 months included self-interviews for sexual behaviors, substance use, and specimen collection for chlamydia, gonorrhea, syphilis, and HIV testing. Changes in behaviors were assessed using the McNemar test, and participants not diagnosed with an STI served as controls for a difference-in-difference (DiD) analysis of changes over time.

Results
Cumulative incidence of an STI was 55% (248 of 447). At 24 months after STI diagnosis, methamphetamine use declined from 50% to 35% (P < 0.01), and median number of sex partners declined from 5 (interquartile range, 2–11) to 2 (interquartile range, 1–6; P < 0.01). Among participants at risk for HIV and diagnosed with an STI (n = 102), postexposure prophylaxis use was 35% and HIV seroconversion was 6%. Based on DiD analyses, participants diagnosed with an STI had higher levels of substance and a higher number of sex partners when compared with those with no STIs; however, declines in these behaviors were comparable to participants not diagnosed with an STI (P
DID > 0.05).

Conclusions
Despite behavior modifications after an STI diagnosis, STI/HIV incidence was high, suggesting that MSM with STIs occupy sexual networks where reductions in sexual and substance using behaviors do not protect them from ongoing exposure to STIs and HIV.
Superiority of 68Ga-FAPI-04 in Delineation of Soft Tissue and Liver Metastases in Chromophobe Renal Cell Carcinoma for Restaging
Authors: Xie Fei , Fu Lilan , Zhou Wenlan 
Published: November 2022

Abstract
Chromophobe renal cell carcinoma (RCC) is a rare tumor. We described findings of 18F-FDG PET/CT and 68Ga-FAPI-04 PET/CT of metastatic chromophobe RCC in a 56-year-old woman. 68Ga-FAPI-04 PET/CT demonstrated that the metastatic lesions in the liver, left posterior abdominal wall, and the left waist had intense uptake of 68Ga-FAPI-04, which was higher than that of 18F-FDG on 18F-FDG PET/CT. 68Ga-FAPI-04 PET/CT also delineated the metastatic lesions more clearly than 18F-FDG PET/CT. This case highlights 68Ga-FAPI-04 PET/CT may be promising in restaging of chromophobe RCC.
Therapeutic Efficacy and Prediction of 18F-FDG PET/CT-Assisted Botulinum Toxin Therapy in Patients With Idiopathic Cervical Dystonia
Authors: Kwon Hye Ryeong , Lee Hyunjong , Sung Duk Hyun , Choi Joon Young 
Published: November 2022

Purpose
This study aimed to investigate the therapeutic efficacy of 18F-FDG PET/CT-assisted botulinum toxin (BTX) injection therapy and predictive PET findings in relation to a good response in patients with idiopathic cervical dystonia (ICD).

Materials and Methods
A total of 78 patients was enrolled from November 2007 to July 2018. The Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS) score was determined at baseline and 4 weeks after BTX injection guided by electromyography and PET/CT. The number of hypermetabolic muscles, the highest SUVmax among hypermetabolic muscles, and the total SUVmax of hypermetabolic muscles were evaluated as pretreatment PET parameters. A good response was defined as a reduction rate ≥30% and a point decrease ≥15 of the TWSTRS total score.

Results
Half of the subjects showed a good response. Good responders had significantly higher baseline TWSTRS scores than poor responders (total score, P < 0.001; severity, P < 0.001; disability, P < 0.001; pain, P = 0.026). Good responders also had significantly higher numbers of hypermetabolic muscles and BTX-injected hypermetabolic muscles (P < 0.001, both). In multivariable analysis, the baseline TWSTRS disability subscale score and the number of BTX-injected hypermetabolic muscles were significant predictors for good response (P = 0.001 and P = 0.028). The aforementioned 3 PET parameters were positively correlated with the baseline TWSTRS scores. In addition, PET/CT well detected dystonic deep cervical muscles.

Conclusions
FDG PET/CT-assisted BTX injection therapy showed good therapeutic efficacy in ICD patients. The numbers of hypermetabolic cervical muscles and BTX-injected hypermetabolic muscles may be helpful in predicting a good response.
The 99mTc-MIP-1404 PSMA Uptake in the Isolated Paratracheal Lymph Node From the Prostate Adenocarcinoma
Authors: Jonusas Justinas , Tiskevicius Sigitas , Janulionis Ernestas 
Published: November 2022

Abstract
The oncologist consulted a 56-year-old man after receiving prostate-specific antigen screening results. Prostate-specific antigen level during the screen time was 33 ng/mL. As a result, poorly differentiated prostate adenocarcinoma with a Gleason score of 9 (5 + 4) was diagnosed. SPECT/CT scan with 99mTc-MIP-1404 PSMA tracer was performed. The 99mTc-PSMA–positive lesions were detected in the prostate, external iliac, obturator lymph nodes of the pelvis, para-aortic, and the right lower paratracheal space. The patient was prescribed androgen deprivation therapy and early chemotherapy with docetaxel (6 fractions), after which radiation therapy to prostate and seminal vesicles was planned.
Increased 68Ga-DOTATATE Uptake in Supraclavicular Brown Adipose Tissue
Authors: Li Li , Li Guannan , Tian Rong , Shen Guohua 
Published: November 2022

Abstract
Characterization of brown adipose tissue (BAT) 18F-FDG uptake has been well reported; however, 68Ga-DOTA–conjugated somatostatin receptor targeting peptides uptake in BAT is rarely documented. Herein, we report an interesting case of increased 68Ga-DOTATATE uptake in supraclavicular BAT in a young boy with paroxysmal hypertension. The low body mass index and increased perfusion of BAT in response to cold may be significant influencing factors.
The Manifestation of a Patient With Myelofibrosis in 68Ga-DOTA-FAPI-04 PET/CT Mimicking “Super Bone Imaging”
Authors: Li Xue , Zhao Qian , Luo Qianfeng , Chen Liming , Huang Zhanwen 
Published: November 2022

Abstract
Primary myelofibrosis is a chronic inflammatory disease of the bone marrow. It progresses from an early robust inflammatory state to a more advanced fibrotic response, representing the advanced stage of the disease. We report a 50-year-old woman who was diagnosed with primary myelofibrosis. 18F-FDG PET/CT showed mild uptake in diffuse sclerotic lesions in the bone matrix, whereas 68Ga-DOTA-FAPI-04 showed intense uptake at the whole skeleton.
Counterdiabatic driving for periodically driven open quantum systems
Authors: Takahashi Kazutaka 
Published: November 2022

We discuss dynamics of periodically driven open quantum systems. The time evolution of the quantum state is described by the quantum master equation, and the form of the dissipator is chosen so that the instantaneous stationary state is given by the Gibbs distribution. We find that the correlation between the population part and the coherence part of the density operator is induced by an adiabatic gauge potential. Although the introduction of the counterdiabatic term eliminates the correlation, additional correlations prevent convergence to the Gibbs distribution. We study the performance of the control by the counterdiabatic term. The system has three different scales and the performance strongly depends on the relations between their magnitudes.
This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Dynamical invariant formalism of shortcuts to adiabaticity
Authors: Takahashi Kazutaka 
Published: November 2022

We give a pedagogical introduction to dynamical invariant formalism of shortcuts to adiabaticity. For a given operator form of the Hamiltonian with undetermined coefficients, the dynamical invariant is introduced to design the coefficients. We discuss how the method allows us to mimic adiabatic dynamics and describe a relation to the counterdiabatic formalism. The equation for the dynamical invariant takes a familiar form and is often used in various fields of physics. We introduce examples of Lax pair, quantum brachistochrone and flow equation.This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Bayes Factors for Two-group Comparisons in Cox Regression with an Application for Reverse-Engineering Raw Data from Summary Statistics
Authors: Linde Maximilian , Tendeiro Jorge N. , van Ravenzwaaij Don 
Published: November 2022

AbstractThe use of Cox proportional hazards regression to analyze time-to-event data is ubiquitous in biomedical research. Typically, the frequentist framework is used to draw conclusions about whether hazards are different between patients in an experimental and a control condition. We offer a procedure to compute Bayes factors for simple Cox models, both for the scenario where the full data are available and for the scenario where only summary statistics are available. The procedure is implemented in our “baymedr” R package. The usage of Bayes factors remedies some shortcomings of frequentist inference and has the potential to save scarce resources.
Altered structural connectome of children with Auditory Processing Disorder: A diffusion MRI study
Authors: Alvand Ashkan , Kuruvilla-Mathew Abin , Roberts Reece P. , Pedersen Mangor , Kirk Ian J. , Purdy Suzanne C. 
Published: November 2022

ABSTRACTAuditory processing disorder (APD) is a listening impairment that some school-aged children may experience as difficulty understanding speech in background noise despite having normal peripheral hearing. Recent resting-state functional magnetic resonance imaging (MRI) has revealed an alteration in regional, but not global, functional brain topology in children with APD. However, little is known about the brain structural organization in APD. We used diffusion MRI data to investigate the structural white matter connectome of 58 children from 8 to 14 years old diagnosed with APD (n=29) and children without hearing complaints (healthy controls, HC; n=29). We investigated the rich-club organization and structural connection differences between APD and HC groups using the network science approach. The APD group showed neither edge-based connectivity differences nor any differences in rich-club organization and connectivity strength (i.e., rich, feeder, local connections) compared to HCs. However, at the regional network level, we observed increased average path length (APL) and betweenness centrality in the right inferior parietal lobule and inferior precentral gyrus, respectively, in children with APD. HCs demonstrated a positive association between APL in the left orbital gyrus and the listening-in-spatialized-noise-sentences task, a measure of auditory processing ability. This correlation was not observed in the APD group. In line with previous functional connectome findings, the current results provide evidence for altered structural networks at a regional level in children with APD, and an association with listening performance, suggesting the involvement of multimodal deficits and a role for structure-function alteration in listening difficulties of children with APD.
mimicINT: a workflow for microbe-host protein interaction inference
Authors: Choteau Sébastien A. , Maldonado Kevin , Bergon Aurélie , Cristianini Marceau , Boujeant Mégane , Drets Lilian , Brun Christine , Spinelli Lionel , Zanzoni Andreas 
Published: November 2022

AbstractBackgroundThe increasing incidence of emerging infectious diseases is posing serious global threats. Therefore, there is a clear need for developing computational methods that can assist and speed up experimental research to better characterize the molecular mechanisms of microbial infections.MethodsIn this context, we developedmimicINT, an open-source computational workflow for large-scale protein-protein interaction inference between microbe and human by detecting putative molecular mimicry elements mediating the interaction with host proteins: short linear motifs (SLiMs) and host-like globular domains.mimicINT exploits these putative elements to infer the interaction with human proteins by using known templates of domain-domain and SLiM-domain interaction templates.mimicINT also provides(i)robust Monte-Carlo simulations to assess the statistical significance of SLiM detection which suffers from false positives, and(ii)an interaction specificity filter to account for differences between motif-binding domains of the same family. We have also mademimicINT available via a web server.ResultsIn two use cases,mimicINT can identify potential interfaces in experimentally detected interaction between pathogenicEscherichia colitype-3 secreted effectors and human proteins and infer biologically relevant interactions between Marburg virus and human proteins.ConclusionsThemimicINT workflow can be instrumental to better understand the molecular details of microbe-host interactions.
Durable Response and Improved CD8 T Cell Plasticity in Lung Cancer Patients After PD1 Blockade and JAK Inhibition
Authors: Mathew Divij , Marmarelis Melina E. , Foley Caitlin , Bauml Joshua M. , Ye Darwin , Ghinnagow Reem , Ngiow Shin Foong , Klapholz Max , Jun Soyeong , Zhang Zhaojun , Zorc Robert , Diehn Maximillian , Hwang Wei-Ting , Zhang Nancy R. , Langer Corey J. , Wherry E. John , Minn Andy J. 
Published: November 2022

ABSTRACTPersistent inflammation including type-one interferon (IFN-I) can cause immunosuppression. We show that delayed administration of the JAK1 inhibitor itacitinib after anti-PD1 improves immune function and anti-tumor response in mice, and results in high response rates (67%) in a phase-2 clinical trial for metastatic non-small cell lung cancer with tumor PDL1≥50%. In contrast to patients with low inflammation who responded to anti-PD1, patients with elevated inflammation had poor immune and tumor responses to anti-PD1 that improved after adding itacitinib. Itacitinib promoted features of CD8 T cell plasticity and therapeutic responses of exhausted and effector-memory clonotypes. Patients with persistent IFN-I signaling refractory to itacitinib showed progressive CD8 T cell terminal differentiation and progressive disease. Thus, JAK inhibition may improve anti-PD1 efficacy by pivoting T cell differentiation dynamics.
Identification of functional immune and neuronal tumour cells in glioma
Authors: Curry Rachel Naomi , McDonald Malcolm F. , Ma Qianqian , Meyer Jochen , Aiba Isamu , Lozzi Brittney , Cervantes Alexis , Ko Yeunjung , Luna-Figueroa Estefania , Choi Dong-Joo , Lee Zhung-Fu , Jing Junzhan , Harmanci Arif O. , Rosenbaum Anna , He Peihao , Mohila Carrie , Jalali Ali , Noebels Jeffrey , Jiang Xiaolong , Deneen Benjamin , Rao Ganesh , Harmanci Akdes Serin 
Published: November 2022

AbstractDespite advances in molecular profiling, therapeutic development has been hindered by the inability to identify and target tumour-specific mechanisms without consequence to healthy tissue. Correspondingly, a computational framework capable of accurately distinguishing tumour from non-tumour cells has yet to be developed and cell annotation algorithms are unable to assign integrated genomic and transcriptional profiles to single cells on a cell-by-cell basis. To address these barriers, we developed the Single Cell Rule Association Mining (SCRAM) tool that integrates RNA-inferred genomic alterations with co-occurring cell type signatures for individual cells. Applying SCRAM to glioma, we identified tumour cell trajectories recapitulate temporally-restricted developmental paradigms and feature unique co-occurring identities. Specifically, we validated two previously unreported tumour cell populations with immune and neuronal signatures as hallmarks of human glioma subtypes.In vivomodeling revealed a rare immune-like tumour cell population resembling antigen presenting cells can direct CD8+ T cell responses. In parallel, Patch sequencing studies in human tumours confirmed that neuronal-like glioma cells fire action potentials and represent 40% ofIDH1mutant tumor cells. These studies identified new glioma cell types with functional properties similar to their non-tumour analogues and demonstrate the ability of SCRAM to identify these cell types in unprecedented detail.
Chikungunya intra-vector dynamics inAedes albopictusfrom Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier’s permissiveness and supports local epidemic potential
Authors: Viginier Barbara , Cappuccio Lucie , Garnier Céline , Martin Edwige , Maisse Carine , Moro Claire Valiente , Minard Guillaume , Fontaine Albin , Lequime Sébastian , Ratinier Maxime , Arnaud Frédérick , Raquin Vincent 
Published: November 2022

AbstractArbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time dependent, quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental and modelling approaches is required to assess arbovirus intra-vector dynamics and estimate epidemic potential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived Aedes albopictus population (Lyon, France) after oral exposure to a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficient CHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% of the infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose. Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and =50% infectious mosquitoes at 6 dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiological simulations conducted with an agent-based model showed that even at low mosquito biting rates, CHIKV could trigger outbreaks locally. Together, this reveals the epidemic potential of CHIKV upon transmission by Aedes albopictus in mainland France.
Deep unfolded convolutional dictionary learning for motif discovery
Authors: Chu Shane , Stormo Gary 
Published: November 2022

AbstractWe present a principled representation learning approach based on convolutional dictionary learning (CDL) for motif discovery. We unroll an iterative algorithm that optimizes CDL as a forward pass in a neural network, resulting in a network that is fully interpretable, fast, and capable of finding motifs in large datasets. Simulated data show that our network is more sensitive and specific for discovering binding sites that exhibit complex binding patterns than popular motif discovery methods such as STREME and HOMER. Our network reveals statistically significant motifs and their diverse binding modes from the JASPAR database that are currently not reported.
Rewarding Value or Prediction Error: Settling the debate over the role of dopamine in reward learning
Authors: Usypchuk Alexandra A. , Maes Etienne JP , Lozzi Megan , Gardner Matthew P.H. , Schoenbaum Geoffrey , Esber Guillem R. , Iordanova Mihaela D. 
Published: November 2022

ABSTRACTThe discovery that DA transients can be mapped onto the reward prediction errors in temporal difference models is a pinnacle achievement of neuroscience. Yet, there is abundant evidence that DA activity reinforces actions, suggesting it serves as an intrinsically rewarding event. These two possibilities are so conceptually intertwined that it is not surprising that they have been so far experimentally conflated. Here, using computational modeling, behavioural blocking and optogenetics, we show that stimulating VTA DA neurons promotes learning even when a natural reward and DA stimulation are held constant across the learning phases of blocking. These findings provide strong evidence in favour of the prediction error hypothesis rather than encoding the rewarding value of appetitive events.