bluuebunny/crossref_metadata_2025 huggingface dataset:
COMBINATION USTEKINUMAB AND VEDOLIZUMAB THERAPY FOR REFRACTORY INFLAMMATORY BOWEL DISEASE: A SINGLE INSTITUTION CASE SERIES
Authors: Dawoud Nabila , Roy Lucas , Elmoursi Ahmed , Elkammar Mahmoud , Eltaher Mohamed , Barrett Terrence , Perry Courtney
Published: January 2022

INTRODUCTION

Over the past 20 years, there have been great strides in the medical management of Inflammatory Bowel Disease (IBD). The advent of anti-TNF mAb therapy was transformative in the management of IBD and the positive effects are well documented1,2,3. While anti-TNF mAb biologics induce and maintain remission in IBD, a substantial portion of patients are refractory4. Newer biologic agents such as ustekinumab (UST) and vedolizumab (VDZ) have expanded therapeutic options for patients; however, obtaining deep remission in a subset of IBD patients remains challenging. We previously reported a successful case of deep remission in a patient with refractory stricturing Crohn’s Disease (CD) treated with maximum dosage UST + VDZ therapy5. Since this report, we have expanded our use of this combination in refractory IBD with encouraging results.

METHODS

Fifteen refractory IBD patients (12 CD, 3 UC) at the University of Kentucky were selected to initiate dual biologic therapy (DBT) with UST and VDZ. All patients previously failed other therapies, but demonstrated partial response to escalated dosing (Q4 week) of either VDZ or UST monotherapy. To determine DBT response, we analyzed fecal calprotectin (FC), C-reactive protein (CRP), albumin, BMI, hemoglobin, Harvey Bradshaw Index (HBI)/Mayo scores, endoscopic and histologic appearance. Steroid-free remission was defined by one or more of the following: 1) endoscopic and histologic remission, 2) normalization of biomarkers (FC and CRP) or 3) clinical remission defined by normalization of clinical scores AND normalization of albumin, hemoglobin, and BMI. Clinical remission was only used when endoscopic or biomarker data was not available.

RESULTS

Among the 12 CD patients receiving dual biologic therapy, 11 met criteria for remission (91.6%). Six of these CD patients had complete endoscopic and histologic remission. Three CD patients did not have follow-up endoscopic or FC data, but did have normalization of albumin, CRP, hemoglobin, and HBI scores. Two CD patients were initiated on DBT for spikes in biomarkers (FC and CRP) despite clinical remission. These biomarkers normalized after initiation of DBT. One of the CD patients did not achieve response, and no one with UC (3 patients) responded. Among the successful cases, the average time to remission was 14.9 weeks. There were no adverse events or safety concerns.

CONCLUSION

Dual biologic therapy with combination ustekinumab and vedolizumab is a promising and safe option for patients with refractory CD, particularly in those who demonstrate a partial response to monotherapy of either agent. This combination was not successful in our UC patients. This case series adds further support for the effectiveness of VDZ+ UST combination therapy in CD. Continued investigation is merited to support routine clinical use and improve access to this combination therapy.
VEDOLIZUMAB AS TREATMENT FOR COMMON VARIABLE IMMUNE DEFICIENCY (CVID): A CASE SERIES AND BRIEF REVIEW OF THE LITERATURE
Authors: Patel Sagar , Wilhoit Cameron , Williams Kelli , Forster Erin
Published: January 2022

INTRODUCTION

Common variable immunodeficiency (CVID) is the most common symptomatic immunodeficiency, frequently presenting as recurrent upper respiratory infections. A portion of these patients develop non-specific gastrointestinal symptoms with a smaller subset developing CVID enteropathy, characterized by chronic diarrhea with absence of plasma cells and aggregates of T cells on intestinal pathology. We describe two cases of steroid refractory CVID enteropathy who were started on Vedolizumab (VDZ) with clinical remission.

CASE 1

A 26 year-old female with primarily sinopulmonary CVID on immunoglobulin (IVIG) who developed profuse diarrhea. Infectious work-up and celiac biopsies were negative. Shortly after, colonoscopy with biopsies showing decreased plasma cells consistent with CVID enteropathy. She was started on budesonide with resolution of symptoms. After two months was weaned to 6 mg and began to have daily diarrhea. She was weaned to 3 mg budesonide daily and began to have more frequent diarrhea, bloating, weight loss. Later, budesonide was increased to 6 mg with no response then maximized to 9 mg daily. She was treated with standard induction and maintenance dosing of VDZ 300 with symptomatic remission. Budesonide was tapered off after completing third dose of vedolizumab. The patient has not had any more weight loss and stools are more formed. Her symptoms are abated until days prior to her next infusion; thus, VDZ interval was changed to every 7 weeks. She has not yet had colonoscopy to assess for mucosal healing but has had discontinuation of glucocorticoids. There were no adverse infectious events.

CASE 2

A 28-year-old female with a known history of CVID enteropathy presented to GI clinic for refractory daily diarrhea despite chronic glucocorticoid therapy. She was diagnosed with CVID in 1998 and takes subcutaneous IVIG regularly. Colonoscopy showed mild chronic focally active ileitis, chronic active colitis. She started budesonide 9 mg; however, developed striae and weaned off budesonide. Subsequently, she was trialed on tacrolimus 0.1 mg/kg BID but suffered body aches and contracted COVID-19. She successively had worsening of stool frequency. Colonoscopy revealed ileum had loss of villous architecture and histologic evidence of CVID. She was treated with standard induction and maintenance dose of VDZ 300 mg with symptomatic remission. Symptoms dramatically improved and repeat endoscopy demonstrated no colitis. There were no adverse infectious events.

DISCUSSION

VDZ is an attractive therapy as the gut selective mechanism of action lowers risk of opportunistic infections and has emerged as an appealing therapeutic choice for this specific population. Some case reports have been mixed efficacy of inducing remission with VDZ; however, we report 2 cases of steroid resistant CVID enteropathy with clinical remission after induction with VDZ.
Daptomycin-Resistant Enterococcus Bacteremia Is Associated With Prior Daptomycin Use and Increased Mortality After Liver Transplantation
Authors: Lee Rachael A , Goldman Jason , Haidar Ghady , Lewis Jessica , Arif Sana , Hand Jonathan , La Hoz Ricardo M , Pouch Stephanie , Holaday Eric , Clauss Heather , Kaye Keith S , Nellore Anoma
Published: January 2022

Background

Risk factors for acquisition of vancomycin-resistant Enterococcus (VRE) include immunosuppression, antibiotic exposure, indwelling catheters, and manipulation of the gastrointestinal tract, all of which occur in liver transplant recipients. VRE infections are documented in liver transplantation (LT); however, only one single center study has assessed the impact of daptomycin-resistant Enterococcus (DRE) in this patient population.

Methods

We conducted a retrospective multicenter cohort study comparing liver transplant recipients with either VRE or DRE bacteremia. The primary outcome was death within 1 year of transplantation. Multivariable logistic regression analyses were performed to calculate adjusted odds ratios for outcomes of interest.

Results

We identified 139 cases of Enterococcus bacteremia following LT, of which 78% were VRE and 22% were DRE. When adjusted for total intensive care unit days in the first transplant year, liver-kidney transplantation, and calcineurin inhibitor use, patients with DRE bacteremia were 2.65 times more likely to die within 1 year of transplantation (adjusted odds ratio [aOR], 2.648; 95% CI, 1.025–6.840; P = .044). Prior daptomycin exposure was found to be an independent predictor of DRE bacteremia (aOR, 30.62; 95% CI, 10.087–92.955; P < .001).

Conclusions

In this multicenter study of LT recipients with Enterococcus bacteremia, DRE bacteremia was associated with higher 1-year mortality rates when compared with VRE bacteremia. Our data provide strong support for dedicated infection prevention and antimicrobial stewardship efforts for transplant patients. Further research is needed to support the development of better antibiotics for DRE and practical guidance focusing on identification and prevention of colonization and subsequent infection in liver transplant recipients at high risk for DRE bacteremia.
Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants
Authors: Tang Haoneng , Ke Yong , Ma Hang , Han Lei , Wang Lei , Zong Huifang , Yuan Yunsheng , Wang Zhenyu , He Yang , Chang Yunsong , Wang Shusheng , Liu Junjun , Yue Yali , Xu Wenbo , Zhang Xiaoju , Wang Ziqi , Yang Li , Chen Hua , Bian Yanlin , Zhang Baohong , Liao Yunji , Yin Haiyang , Chen Yi , Zhang En , Zhang Xiaoxiao , Jiang Hua , Xie Yueqing , Gilly John , Wu Mingyuan , Sun Tao , Zhu Jianwei
Published: January 2022

Emerging SARS-CoV-2 variants are threatening the efficacy of antibody therapies. Combination treatments including ACE2-Fc have been developed to overcome the evasion of neutralizing antibodies (NAbs) in individual cases. Here we conducted a comprehensive evaluation of this strategy by combining ACE2-Fc with NAbs of diverse epitopes on the RBD. NAb+ACE2-Fc combinations efficiently neutralized HIV-based pseudovirus carrying the spike protein of the Delta or Omicron variants, achieving a balance between efficacy and breadth. In an antibody escape assay using replication-competent VSV-SARS-CoV-2-S, all the combinations had no escape after fifteen passages. By comparison, all the NAbs without combo with ACE2-Fc had escaped within six passages. Further, the VSV-S variants escaped from NAbs were neutralized by ACE2-Fc, revealing the mechanism of NAb+ACE2-Fc combinations survived after fifteen passages. We finally examined ACE2-Fc neutralization against pseudovirus variants that were resistant to the therapeutic antibodies currently in clinic. Our results suggest ACE2-Fc is a universal combination partner to combat SARS-CoV-2 variants including Delta and Omicron.
Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City
Authors: Wertheim Joel O. , Wang Jade C. , Leelawong Mindy , Martin Darren P. , Havens Jennifer L. , Chowdhury Moinuddin A. , Pekar Jonathan , Amin Helly , Arroyo Anthony , Awandare Gordon A. , Chow Hoi Yan , Gonzalez Edimarlyn , Luoma Elizabeth , Morang’a Collins M. , Nekrutenko Anton , Shank Stephen D. , Quashie Peter K. , Rakeman Jennifer L. , Ruiz Victoria , Torian Lucia V. , Vasylyeva Tetyana I. , Kosakovsky Pond Sergei L. , Hughes Scott
Published: January 2022

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts revealed that Alpha variant alleles comprised between 70-80% of the genomes, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Further investigation revealed the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.
A mixed method study on supportive supervision of Community Health Workers from Central India
Authors: Revadi G , Joshi Ankur , Pakhare Abhijit P
Published: January 2022

Introduction

Supportive supervision of the Community health workers (CHWs) are critical for their efficient functioning in various health programs. CHWs in India are supervised by facilitators known as ASHA Sahyogini. Our study aimed at investigating the linkage between knowledge and skills of CHW facilitators and their CHWs. To understand the problems encountered by the CHW facilitators while assisting their CHWs. Also, to determine the perceptions of CHWs on nature of supportive supervision of their facilitators.

Methods

A mixed method explanatory study using purposive sampling was conducted in a rural block of Madhya Pradesh (Central India). The CHWs were categorised into relatively high performing (RHP) and relatively low performing (RLP) groups based on their performance-based incentives received during (2017-2018). Quantitative component comprised of self-administered questionnaire and skill assessment while the qualitative component comprised of three focussed group discussion with RHP, RLP CHWs and their facilitators.

Results

The mean (SD) supportive supervision score given by CHW facilitators were found to be significantly associated with CHWs performance. Problems faced by CHW facilitators while assisting their CHWs resulted from inadequate education of CHWs, insufficient incentives, transport problems and repetitive surveys. While some CHWs perceived to have received good assistance from their facilitators, there were a few who were not dependant on their facilitators and executed duties by self.

Conclusion

CHWs performance cannot be ascribed completely to the CHW facilitators performance. The challenges perceived by CHW facilitators were unmodifiable and requires them to strongly motivate and support their CHWs in order to improve their functionality.
Effectiveness of BNT162b2 and mRNA-1273 COVID-19 boosters against SARS-CoV-2 Omicron (B.1.1.529) infection in Qatar
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , AlMukdad Sawsan , Tang Patrick , Hasan Mohammad R. , Coyle Peter , Yassine Hadi M. , Al-Khatib Hebah A. , Smatti Maria K. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto
Published: January 2022

BACKGROUND

Waning of COVID-19 vaccine protection and emergence of SARS-CoV-2 Omicron (B.1.1.529) variant have expedited efforts to scale up booster vaccination. This study compared protection afforded by booster doses of the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines, compared to the primary series of only two doses in Qatar, during a large, rapidly growing Omicron wave.

METHODS

In a population of 2,232,224 vaccinated persons with at least two doses, two matched, retrospective cohort studies were implemented to investigate effectiveness of booster vaccination against symptomatic SARS-CoV-2 infection and against COVID-19 hospitalization and death, up to January 9, 2022. Association of booster status with infection was estimated using Cox proportional-hazards regression models.

RESULTS

For BNT162b2, cumulative symptomatic infection incidence was 2.9% (95% CI: 2.8-3.1%) in the booster-dose cohort and 5.5% (95% CI: 5.3-5.7%) in the primary-series cohort, after 49 days of follow-up. Adjusted hazard ratio for symptomatic infection was 0.50 (95% CI: 0.47-0.53). Booster effectiveness relative to primary series was 50.1% (95% CI: 47.3-52.8%). For mRNA-1273, cumulative symptomatic infection incidence was 1.9% (95% CI: 1.7-2.2%) in the booster-dose cohort and 3.5% (95% CI: 3.2-3.9%) in the primary-series cohort, after 35 days of follow-up. The adjusted hazard ratio for symptomatic infection was 0.49 (95% CI: 0.43-0.57). Booster effectiveness relative to primary series was 50.8% (95% CI: 43.4-57.3%). There were fewer cases of severe COVID-19 in booster-dose cohorts than in primary-series cohorts, but cases of severe COVID-19 were rare in all cohorts.

CONCLUSIONS

mRNA booster vaccination is associated with modest effectiveness against symptomatic infection with Omicron. The development of a new generation of vaccines targeting a broad range of variants may be warranted.
Mapping cherry blossoms from geotagged street-level photos
Authors: Funada Shuya , Tsutsumida Narumasa
Published: January 2022

Floral phenology is useful information as an indicator on climate change and ecosystem services, however its observation is not straightforward over space and time. Satellite remote sensing and official and volunteer-based in-situ observations have been conducting, but the long-term and accurate data collection is challenging due to the insufficient quality and quantity of observations and the lack of financial and human resources to sustain. Here, we demonstrate a flower detection model from street-level photos, which can be the core function of a semi-automatic observation system to tackle those issues above. We detected cherry blossoms by this model from geotagged images with the observation date, obtained from Mapillary, which is one of social sensing data sources, and mapped dates of flowering in a study site, Aizuwakamatsu, Japan in April 2018. This approach enables us to collect floral phenology information semi-automatically as a data-driven approach. It is expected to collect a large number of observations with a certain level of quality by avoiding human-induced biases for the observations.
Stabilization of E-cadherin adhesions by COX-2/GSK3β signaling is a targetable pathway in metastatic breast cancer
Authors: Balamurugan Kuppusamy , Sehareen Saadiya , Sharan Shikha , Krishnamurthy Savitri , Tang Wei , McKennett Lois , Padmanaban Veena , Czarra Kelli , Ewald Andrew J. , Ueno Naoto T. , Ambs Stefan , Poria Dipak K. , Sterneck Esta
Published: January 2022

Metastatic progression and treatment-resistance of breast cancer has been associated with epithelial-mesenchymal-transition including downregulation of E-cadherin (CDH1) expression, which can be initiated by inflammatory mediators such as COX-2. Recently, E-cadherin-mediated, cluster-based metastasis and treatment resistance has become more appreciated, though the mechanisms that maintain E-cadherin expression in this context are unknown. Through studies of inflammatory breast cancer and anin vitrotumor cell emboli culture paradigm, we identified a role for COX-2, a target gene of C/EBPδ, or its metabolite PGE2 in promoting protein stability of E-cadherin, β-catenin and p120 catenin through inhibition of GSK3β, without affectingCDH1mRNA. The COX-2 inhibitor celecoxib downregulated E-cadherin complex proteins and caused cell death. Co-expression of E-cadherin and COX-2 was seen in breast cancer patients with poor outcome and, along with inhibitory GSK3β phosphorylation, in patient-derived xenografts of triple negative breast cancer. Celecoxib alone decreased E-cadherin protein expression within xenograft tumors, reduced circulating tumor cells and clusters, and in combination with paclitaxel attenuated or regressed lung metastases. This study uncovered a mechanism by which metastatic breast cancer cells can maintain E-cadherin-mediated cell-cell adhesions and cell survival, suggesting that patients with COX-2+/E-cadherin+ breast cancer may benefit from targeting of the PGE2 signaling pathway.
Bergmann’s rule inMicrolophuslizards: testing for latitudinal and climatic gradients of body size
Authors: Toyama Ken S. , Boccia Christopher K.
Published: January 2022

Broadscale environmental gradients exert selection pressures that can result in macroevolutionary patterns of phenotypic diversity. Bergmann’s rule, one of the most studied ecogeographical patterns, states that among related species or populations, larger body sizes should occur at higher latitudes or colder climates given the efficacy of larger sizes to conserve heat. However, there is still much debate regarding the mechanisms that underlie the rule and whether they should be different between endotherms and ectotherms. Here we test for Bergmann’s rule inMicrolophuslizards, a genus distributed in western South America and the Galápagos Islands, and test for associations between body size and climatic variables. Our results indicate that mainlandMicrolophusspecies follow Bergmann’s rule, meaning that larger species are found towards the southernmost latitudes encompassed by the genus’ distribution. This relationship was similar for males and females, suggesting that patterns of sexual size dimorphism are not driven by differing latitudinal gradients of body size between the sexes. We identified negative associations between body size and temperature, precipitation, and isothermality, meaning that larger species are found in colder, drier, and more thermally variable environments. We discuss the possible mechanisms behind this pattern, the implications of insularity and ecology for the evolution of body size in this genus, and emphasize the need for additional natural history information to allow for the elucidation of the mechanisms behind the patterns presented in this work.
Phylogenetic analyses of AGO/DCL/RDR proteins in green plants refine the evolution of small RNA pathways
Authors: Bélanger Sébastien , Zhan Junpeng , Meyers Blake C.
Published: January 2022

Several protein families play a role in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-directed RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back toAcorus americanus, the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events ofAGOgenes that were lost, retained or further duplicated in sub-groups, indicating that the evolution ofAGOsis complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17 and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins provide insights into the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.
Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser
Authors: Li Daofeng , Purushotham Deepak , Harrison Jessica K. , Wang Ting
Published: January 2022

Biological functions are not only encoded by the genome’s sequence but also regulated by its three-dimensional (3D) structure. More and more studies have revealed the importance of 3D chromatin structures in development and diseases; therefore, visualizing the connections between genome sequence, epigenomic dynamics (1D) and the 3D genome becomes a pressing need. The WashU Epigenome Browser introduces a new 3D visualization module to integrate visualization of 1D (such as sequence features, epigenomic data) and 2D data (such as chromosome conformation capture data) with 3D genome structure. Genomic coordinates are encoded in 3D models of the chromosomes; thus, all genomic information displayed on a 1D genome browser can be visualized on a 3D model, supported by genome browser utilities and facilitating interpretation of genomic data. Biological information that is difficult to illustrate in 1D becomes more intuitive when displayed in 3D, providing novel and powerful tools for investigators to hypothesize and understand the connections between biological functions and 3D genome structures.
A systematic review of the factors associated with suicide attempts among sexual-minority adolescents
Authors: Wang Xavier , Gan Quan , Zhou Junwen , Cosquer Mireille , Falissard Bruno , Corruble Emmanuelle , Jousselme Catherine , Gressier Florence
Published: January 2022

Introduction

Suicide attempt is a worldwide major public health problem, that accounts for 1.4% of all deaths worldwide Recent literature reported higher risk of suicide attempt among adolescents associated with sexual minority status but few systematic reviews focused on the risk and protective factors. For that reason, it seems necessary to examine risk and protective factors of attempted suicide in sexual minority adolescents.

Methods

We conducted a systematic review of published studies on factors associated with suicide attempts in LGBT adolescents. 4 databases up to December 2020 were searched to find relevant studies.

Results

In addition to the factors usually found in general population (gender, ethnic minorities, childhood trauma, psychiatric symptoms, addictive behaviors), some factors have been independently associated with suicide attempt in LGBT population: early coming out, not acceptable by families, not satisfied with LGBT friendship, too few number of friends, physical abuse, sexual abuse and bullying. The protective factors of suicide attempt reported in LGBT population were feeling safety at school, teacher support, anti-bullying policy, and other adult’s support.

Conclusion

Effective preventive measures for suicide attempt among LGBT youth need to be developed and implemented. The impact of interventions targeting teacher responses to LGBT stigma, discussion of LGBT issues in class and reactions of family and friends to the coming out of LGBT youth should be further investigated.
Developing all-in-one virus-like particles for Cas9 mRNA/single guide RNA co-delivery and aptamer-containing lentiviral vectors for improved gene expression
Authors: Yadav Manish , Atala Anthony , Lu Baisong
Published: January 2022

Lentiviral vectors (LVs) are widely used for delivering foreign genes for long-term expression. Normal LVs contain the RNA genome, which is reverse transcribed into DNA and integrates into the host genome to mediate long-term gene expression. Recently, virus-like particles (VLPs) were developed for mRNA delivery. In these VLPs, packaging mRNA into the particles is achieved via interactions between the aptamer and aptamer-binding protein (ABP), and mRNA is not reverse transcribed or integrated. These VLPs are useful for delivering Cas9 mRNA for short-term endonuclease expression. Generating high-titer normal integrating LVs is challenging. Until recently, VLPs were not efficient for co-delivering Cas9 mRNA and single guide RNA (sgRNA). By fusing ABP to the N-terminus of HIV Gag protein, hybrid particles were developed to co-deliver Cas9 mRNA and sgRNA. But the method for modifying Gag impaired particle assembly. Previously we found that adding an ABP after the second zinc finger domain of nucleocapsid (NC) protein had minimal effects on particle assembly. Based on this observation, we developed hybrid particles to co-deliver Cas9 mRNA and sgRNA. We further improved LVs for integrated gene expression by including an aptamer sequence in lentiviral transfer plasmids, which improved lentiviral particle production and enhanced LV genomic RNA packaging. In summary, we describe development of new all-in-one VLPs for co-delivery of Cas9 mRNA and sgRNA and new LVs for enhanced vector production and gene expression.
Pathogen Detection in RNA-Seq Data with Pathonoia
Authors: Liebhoff Anna-Maria , Menden Kevin , Laschtowitz Alena , Franke Andre , Schramm Christoph , Bonn Stefan
Published: January 2022

Motivation

Recent evidence suggests that bacterial and viral infections may cause or exacerbate many human diseases. One method of choice to detect microbes in tissue is RNA sequencing. While the detection of specific microbes using RNA sequencing offers good sensitivity and specificity, untargeted approaches suffer from very high false positive rates and a lack of sensitivity for lowly abundant organisms.

Results

We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host cell interactions by correlating the microbial to host gene expression. Pathonoia outperforms competing algorithms in microbial detection specificity, both on in silico and real datasets. Lastly, we present two case studies in human liver and brain in which microbial infection might exacerbate disease.

Availability

A Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub https://github.com/kepsi/Pathonoia.

Contact

aliebho1@jhu.edu and s.bonn@uke.de

Graphical Abstract
Adipose tissue dysfunction and visceral fat are associated to hepatic insulin resistance and severity of NASH even in lean individuals
Authors: Saponaro Chiara , Sabatini Silvia , Gaggini Melania , Carli Fabrizia , Rosso Chiara , Positano Vincenzo , Armandi Angelo , Caviglia Gian Paolo , Faletti Riccardo , Bugianesi Elisabetta , Gastaldelli Amalia
Published: January 2022

Background & Aims

Nonalcoholic fatty liver disease (NAFLD) is a heterogeneous disorder, but the factors that determine this heterogeneity remain poorly understood. Adipose tissue (AT) dysfunction is causally linked to NAFLD since it causes intrahepatic triglyceride (IHTG) accumulation through increased hepatic lipid flow, due to insulin resistance (IR) and pro-inflammatory adipokines release. While many studies in NAFLD have looked at total adiposity (that is mainly subcutaneous fat, SC-AT), it is still unclear the impact of visceral fat (VF). Thus, we investigated how VF vs. SC-AT were related to NAFLD in lean, overweight, and obese individuals compared to lean controls.

Methods

Thirty-four non-diabetic NAFLD with liver biopsy and eight lean control individuals (CT) were enrolled in this study. We measured fat distribution (VF, SC-AT and IHTG) by magnetic resonance imaging (MRI), adiponectin concentration, free fatty acids (FFAs) and triglyceride (TAG) concentration and composition by mass spectrometry (MS), lipolysis and IR by tracer infusion.

Results

IHTG was positively associated with lipolysis, adipose tissue IR, TG concentrations, and increased ratio of saturated/unsaturated fatty acids. VF was higher in NAFLD (including lean individuals) compared to controls, was increased with fibrosis stage and was associated with IR in liver, muscle and adipose tissue, increased lipolysis, and decreased adiponectin levels. Collectively, our results suggest that VF accumulation, given its location close to the liver, is one of the major risk factors for NAFLD.

Conclusions

These findings propose VF as an early indicator of NAFLD independently of BMI, which may allow for evidence-based prevention and intervention strategies.
A GSVA based gene set synergizing with CD4+T cell bearing harmful factors yield risk signals in HBV related diseases via amalgamation of artificial intelligence
Authors: Huang Jun , Zhao Chunbei , Zhang Xinhe , Zhao Qiaohui , Zhang Yanting , Chen Liping , Dai Guifu
Published: January 2022

Genes encoding chemokines and extracellular matrix (ECM) play pivotal roles in chronic HBV infection (CHB), HBV related fibrosis (HBV-LF) and hepatocellular carcinoma (HBV-HCC). The landscape and potential of these genes in prognosis across diseases stages have not been fully and systemically understood. In this study, we defined an HBV-LF associated gene set comprised of chemokines and ECM related genes directly induced by initial HBV infection through GSVA algorithm that named as CLST (C stands for CXCL9, CXCL10, CCL19 and CCL20; L for LUM; S for SOX9 and SPP1; T for THBS1, THBS2) and evaluated its biomarker values in CHB and HBV-LF. Enrichment scores (ES) of CLST was subsequently observed synergized with activated CD4+T cells (aCD4) highly related to T helper cell 17 (TH17) associated genes and immune checkpoints and addressed as risk signals due to bearing harmful prognosis factors in tumor tissues of patients with HBV-HCC. Dual higher enrichment score (ES) of CLST and aCD4 in HBV-HCC patients exhibited worse overall survival (OS). Feature genes specific to these two gene sets showed promising clinical relevance in early-stage of HBV-HCC definition and OS prediction incorporating laboratory parameters via artificial intelligence (AI) systems. Finally, a novel mechanistic insight into the issue was proposed that PEG IFN-α as an immunotherapy through modulating CLST signal in treatment responders and these immune signals down-regulation could be beneficial for HBV related diseases control and prevention. Together, our study provides GSVA and AI derived immunogenomic prognosis signatures and clinical utility of these signals will be benefit for HBV related diseases cure.
Behavioral and neurochemical effects of novel N-Benzyl-2-phenylethylamine derivatives in adult zebrafish
Authors: Demin Konstantin A. , Kupriyanova Olga V. , Shevyrin Vadim A. , Derzhavina Ksenia A. , Krotova Nataliya A. , Ilyin Nikita P. , Kolesnikova Tatiana O. , Galstyan David S. , Kositsyn Iurii M. , Khaybaev Abubakar-Askhab S. , Seredinskaya Maria V. , Dubrovskii Yaroslav , Sadykova Raziya G. , Nerush Maria O. , Mor Mikael S. , Petersen Elena V. , Strekalova Tatyana , Efimova Evgeniya V. , Bozhko Dmitrii V. , Myrov Vladislav O. , Kolchanova Sofia M. , Polovian Aleksander I. , Galumov Georgii K. , Kalueff Allan V.
Published: January 2022

Serotonergic hallucinogenic drugs potently affect human brain and behavior, and have recently emerged as potentially promising agents in psychopharmacotherapy. Complementing rodent studies, zebrafish (Danio rerio) is a powerful animal model for screening neuroactive drugs, including serotonergic agents. Here, we test ten different N-Benzyl-2-phenylethylamine (NBPEA) derivatives with the 2,4- and 3,4-dimethoxy substitutions in the phenethylamine moiety and the - OCH3, -OCF3, -F, -Cl and -Br substitutions in theorthoposition of phenyl ring ofN-benzyl fragment, assessing their behavioral and neurochemical effects in adult zebrafish. Overall, substitutions inN-benzyl fragment primarily affected zebrafish locomotion, and in phenethylamine moiety - anxiety-like behavior, also modulating brain serotonin and/or dopamine turnover. We also identified several behavioral clusters, including anxiogenic/hypolocomotor (24H-NBF, 24H-NBOMe and 34H-NBF), behaviorally inert (34H-NBBr, 34H-NBCl and 34H- NBOMe), anxiogenic/hallucinogenic-like (24H-NBBr, 24H-NBCl and 24H-NBOMe(F)), and anxiolytic/hallucinogenic-like (34H-NBOMe(F)) agents. The 24H-NBOMe(F) and 34H-NBOMe(F) also reduced despair-like behavior in zebrafish. The artificial intelligence-driven phenotyping supports association of multiple compounds with NMDA antagonists and/or MDMA, supporting their potential hallucinogenic-like properties, as well as other valuable psychoactive effects.In silicofunctional molecular activity modelling also supports existing of similarities between studied NBPEAs drugs, MDMA, and ketamine. Functional analysis implicates potential involvement of serotonin release stimulating activity, calcium channel (voltage-sensitive) activity, some serotonin receptors activity and variety of psychiatric and neurologic disorders treatments activities. Overall, we report potent neuroactive properties of several novel syntheticN-benzylphenylethylamines in anin vivovertebrate model system (zebrafish), raising the possibility of their potential use in clinical practice.
Phenotypic dissection of epithelial lineages and therapeutic manipulation of differentiation programs in human Adenoid Cystic Carcinomas (ACCs)
Authors: Viragova Sara , Aparicio Luis , Zhao Junfei , Valencia Salazar Luis E. , Schurer Alexandra , Dhuri Anika , Sahoo Debashis , Moskaluk Christopher A. , Rabadan Raul , Dalerba Piero
Published: January 2022

Adenoid Cystic Carcinoma (ACC) is a rare and aggressive form of salivary gland cancer, characterized by the co-existence within tumor tissues of two distinct populations of malignant cells, phenotypically similar to the myoepithelial and ductal lineages of normal salivary glands. Using a novel computational approach for single-cell RNA-seq analysis, we identified two cell-surface markers (CD49f, KIT) that enable the differential purification of myoepithelial-like (CD49fhigh/KITneg) and ductal-like (CD49flow/KIT+) cells from ACC patient derived xenografts (PDX). Using prospective xeno-transplantation experiments, we demonstrate that myoepithelial-like cells act as progenitors of ductal-like cells. Using three-dimensional (3D) organoid cultures, we demonstrate that agonists of retinoic acid (RA) signaling promote differentiation of myoepithelial-like cells into ductal-like cells, while inhibitors of RA signaling selectively kill ductal-like cells. Finally, we demonstrate that BMS493, an inverse agonist of RA signaling, can be successfully leveraged for the in vivo treatment of human ACCs.
Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12
Authors: Wang Zixiang , Wang Shourong , Qin Junchao , Zhang Xiyu , Lu Gang , Liu Hongbin , Guo Haiyang , Wu Ligang , Shao Changshun , Kong Beihua , Liu Zhaojian
Published: January 2022

Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a challenge to identify the cancer-specific splicing variants. Here we demonstrated that spliceosome component BUD31 is increased in ovarian cancer, and its higher expression predicts worse prognosis. We characterized the BUD31 binding motif and found that BUD31 preferentially binds exon-intron regions near splicing sites by CLIP-seq. Further analysis revealed that BUD31 inhibition results in extensive exon skipping and decreased abundance of long CDS isoforms. In particular, we identified BCL2L12, an anti-apoptotic BCL2 family member, as a functional splicing target of BUD31. BUD31 stimulates the inclusion of exon 3 to generate full-length BCL2L12 and promotes ovarian cancer progression. Knockdown of BUD31 or splice-switching antisense oligonucleotide treatment promotes exon 3 skipping and results in a truncated isoform of BCL2L12 that undergoes nonsense-mediated mRNA decay, and the cells subsequently undergo apoptosis. Our findings reveal BUD31-regulated exon inclusion as a critical factor in ovarian cancer cell survival and progression.
MOJITOO: a fast and universal method for integration of multimodal single cell data
Authors: Cheng Mingbo , Li Zhijian , Costa Ivan G.
Published: January 2022

The advent of multi-modal single cell sequencing techniques have shed new light on molecular mechanisms by simultaneously inspecting transcriptomes, epigenomes and proteomes of the same cell. However, to date, the existing computational approaches for integration of multimodal single cell data are either computationally expensive, require the delineation of parameters or can only be applied to particular modalities.

We present a single cell multi-modal integration method, named MOJITOO (Multi-mOdal Joint IntegraTion of cOmpOnents). MOJITOO uses canonical correlation analysis for a fast and parameter free detection of a shared representation of cells from multimodal single cell data. Moreover, estimated canonical components can be used for interpretation, i.e. association of modality specific molecular features with the latent space. We evaluate MOJITOO using bi- and tri-modal single cell data sets and show that MOJITOO outperforms existing methods regarding computational requirements, preservation of original latent spaces and clustering.
Implicit adaptation is modulated by the relevance of feedback
Authors: Parvin Darius E. , Tsay Jonathan , Dang Kristy V. , Stover Alissa R. , Ivry Richard B. , Morehead J. Ryan
Published: January 2022

Given that informative and relevant feedback in the real world is often intertwined with distracting and irrelevant feedback, we asked how the relevancy of visual feedback impacts implicit sensorimotor adaptation. To tackle this question, we presented multiple cursors as visual feedback in a center-out reaching task and varied the task relevance of these cursors. In other words, participants were instructed to hit a target with a specific task-relevant cursor, while ignoring the other cursors. In Experiment 1, we found that reach aftereffects were attenuated by the mere presence of distracting cursors, compared to reach aftereffects in response to a single task-relevant cursor. The degree of attenuation did not depend on the position of the distracting cursors. In Experiment 2, we examined the interaction between task relevance and attention. Participants were asked to adapt to a task-relevant cursor/target pair, while ignoring the task-irrelevant cursor/target pair. Critically, we jittered the location of the relevant and irrelevant target in an uncorrelated manner, allowing us to index attention via how well participants tracked the position of target. We found that participants who were better at tracking the task-relevant target/cursor pair showed greater aftereffects, and interestingly, the same correlation applied to the task-irrelevant target/cursor pair. Together, these results highlight a novel role of task relevancy on modulating implicit adaptation, perhaps by giving greater attention to informative sources of feedback, increasing the saliency of the sensory prediction error.
Ultra-flexible and Stretchable Intrafascicular Peripheral Nerve Recording Device with Axon-dimension, Cuff-less Microneedle Electrode Array
Authors: Yan Dongxiao , Jiman Ahmad A. , Bottorff Elizabeth C. , Patel Paras R. , Meli Dilara , Welle Elissa J. , Ratze David C. , Havton Leif A. , Chestek Cynthia A. , Kemp Stephen W.P. , Bruns Tim M. , Yoon Euisik , Seymour John
Published: January 2022

Peripheral nerve mapping tools with higher spatial resolution are needed to advance systems neuroscience, and potentially provide a closed-loop biomarker in neuromodulation applications. Two critical challenges of microscale neural interfaces are (i) how to apply them to small peripheral nerves, and (ii) how to minimize chronic reactivity. We developed a flexible microneedle nerve array (MINA), which is the first high-density penetrating electrode array made with axon-sized silicon microneedles embedded in low-modulus thin silicone. We present the design, fabrication, acute recording, and chronic reactivity to an implanted MINA. Distinctive units were identified in the rat peroneal nerve. We also demonstrate a long-term, cuff-free, and suture-free fixation manner using rose bengal as a light-activated adhesive for two timepoints. The tissue response at 1-week included a sham (N=5) and MINA-implanted (N=5) group, and the response at 6-week also included a sham (N=3) and MINA-implanted (N=4) group. These conditions were quantified in the left vagus nerve of rats using histomorphometry. Micro-CT was added to visualize and quantify tissue encapsulation around the implant. MINA demonstrated a reduction in encapsulation thickness over previously quantified interfascicular methods. Future challenges include techniques for precise insertion of the microneedle electrodes and demonstrating long-term recording.
Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection
Authors: Zong Wei , Seney Marianne L. , Ketchesin Kyle D. , Gorczyca Michael T. , Liu Andrew C. , Esser Karyn A. , Tseng George C. , McClung Colleen A. , Huo Zhiguang
Published: January 2022

Circadian clocks are 24-hour endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub (https://github.com/circaPower/circaPower).
Quantifying the effects of recent glacial history and future climate change on a unique population of mountain goats
Authors: Young Kiana B. , Lewis Tania M. , White Kevin S. , Shafer Aaron B.A.
Published: January 2022

Human disturbance and climate change can impact populations by disrupting movement corridors and reducing important habitat. Characterizing how animals respond to such environmental changes is valuable for conservation as many species, especially habitat specialists, can experience reduced genetic diversity when deleterious habitat change occurs, leading to an increased likelihood of extirpation. Mountain goats (Oreamnos americanus) exemplify this conservation challenge; their geographically isolated habitat can inhibit gene flow, making them susceptible to population declines in the face of anthropogenic-induced landscape change. To facilitate biologically informed population management of mountain goats in Glacier Bay National Park, Alaska, we characterized the fine-scale genetic population structure and examined how future climate change could impact the population density of these mountain goats. We used DNA samples to estimate diversity and depict the genealogical history. Climate response models allowed us to simulate changes to suitable habitat and predict how this might influence future population structure. Our results indicated that three genetically distinct subpopulations exist in Glacier Bay and that the population structure is reflective of the historic landscape patterns. Climate modeling predicted that demographic productivity was likely to be reduced for all subpopulations; additionally, we found that climate change likely degrades the suitability of movement corridors that facilitate gene flow between subpopulations, ultimately increasing the cost of travel. Understanding such fine-scale patterns are key to managing subpopulations, particularly with impending changes to the landscape.