bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica
Authors: Sun Yanan , Sun Jin , Yang Yi , Lan Yi , Ip Jack Chi-Ho , Wong Wai Chuen , Kwan Yick Hang , Zhang Yanjie , Han Zhuang , Qiu Jian-Wen , Qian Pei-Yuan
Published: July 2021

Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.
Interposition Grafting of the Facial Nerve After Resection of a Large Facial Nerve Schwannoma: 2-Dimensional Operative Video
Authors: Ibn Essayed Walid , Aboud Emad , Al-Mefty Ossama
Published: July 2021

Facial nerve schwannomas can develop at any portion of the facial nerve.
1
When arising from the mastoid portion of the facial nerve, the tumor will progressively erode the mastoid, giving the schwannoma an aggressive radiological appearance.
1,2
The facial nerve is frequently already paralyzed, or no fascicles can be saved during resection. In these cases, end-to-end interposition grafting is the best option for facial reanimation.
1,3-5
The healthy proximal and distal facial nerves are prepared prior to grafting. The great auricular nerve is readily available near the surgical site and represents an excellent graft donor with minimal associated morbidity.
4,6
We demonstrate this technique through a case of a 48-yr-old male who presented with a complete right-sided facial nerve palsy due to a large facial schwannoma that invaded the mastoid and extended to the hypoglossal canal, causing hypoglossal nerve paralysis, and petrous carotid canal. His 4-yr follow-up showed no recurrent tumor with restored facial nerve function palsy to a House-Brackman grade III, and full recovery of his hypoglossal nerve function.

The patient consented to the surgery and the publication of his image.
Artificial intelligence and productivity: an intangible assets approach
Authors: Corrado Carol , Haskel Jonathan , Jona-Lasinio Cecilia
Published: July 2021

Can artificial intelligence (AI) raise productivity? If we regard AI as a combination of software, hardware, and database use, then it can be modelled as a combination of the deployment of intangible and tangible assets. Since some are measured and some are not, then conventional productivity analysis might miss the contribution of AI. We set out whether there is any evidence to support this view.
The Association Between Chronic Pain Conditions and Subclinical and Clinical Anxiety Among Community-Dwelling Older Adults Consulting in Primary Care
Authors: D’Aiuto Carina , Gamm Simone , Grenier Sébastien , Vasiliadis Helen-Maria
Published: July 2021

Objective

To examine associations between chronic pain conditions, pain level, and subclinical/clinical anxiety in community-dwelling older adults.

Design

Cross-sectional associations were analyzed using multinomial logistic regression to compare the odds of having subclinical/clinical anxiety by painful condition and pain level, controlling for confounders.

Setting

Participants were recruited in primary care waiting rooms to take part in the first wave of the Étude sur la Santé des Aînés (ESA)-Services study.

Subjects

In total, 1,608 older adults aged 65+.

Methods

Clinical anxiety was assessed using DSM-IV criteria. Subclinical anxiety was considered present when participants endorsed symptoms of anxiety but did not fulfill clinical diagnostic criteria for an anxiety disorder. Painful chronic conditions included arthritis, musculoskeletal conditions, gastrointestinal problems, and headaches/migraines. Presence of painful conditions was assessed using combined self-report and health administrative data sources. Pain level was self-reported on an ordinal scale. Physical comorbidities were identified from ICD-9/10 diagnostic codes and depression was evaluated based on the DSM-IV.

Results

Sixty-six percent of home-living older adults suffer from a chronic pain condition. Older adults with clinical anxiety are more likely to experience musculoskeletal pain, gastrointestinal problems, headaches/migraines, and higher pain levels compared to those with no anxiety. Also, those with ≥3 painful conditions are at greater risk for subclinical and clinical anxiety compared to those with no painful condition.

Conclusions

These results emphasize the need for assessing anxiety symptoms in older adults with chronic pain conditions. Comprehensive management of comorbid chronic pain and psychopathology might help reduce the burden for patients and the healthcare system.
Parenthood, Gender, and the Risks and Consequences of Job Loss
Authors: Fuller Sylvia , Qian Yue
Published: July 2021

Job loss can be difficult to navigate for individuals and their families. However, we know very little about the relationship between parental status and job loss. Drawing on rich data from Statistics Canada’s Workplace and Employee Survey, we analyse differences across gender and parental status groups in both risks of job loss and its consequences: re-employment, unemployment, and quality of new jobs relative to those that were lost. We find that parenthood reduces the probability of job loss for prime-age men with young children, but only when employer discretion is involved. This advantage is not shared by otherwise similar mothers or fathers of school-aged children, suggesting that employers are particularly sympathetic to risks to men’s breadwinning role in the early years of fatherhood. Despite similar risks of job loss relative to other groups, mothers of young children are the least likely to be re-employed in the subsequent year, mainly because of their higher levels of labour market withdrawal rather than unemployment. Holding out for “family friendly” work arrangements does not seem to account for this pattern. Overall, our results show that the risks and consequences of job loss strengthen connection to employment for fathers of young children while weakening connection for mothers. Job loss dynamics thus not only reflect but also reinforce asymmetrical breadwinning and caring roles for mothers and fathers of preschool-aged children.
Measuring Splash Dispersal of a Major Wheat Pathogen in the Field
Authors: Karisto Petteri , Suffert Frédéric , Mikaberidze Alexey
Published: July 2021

Capacity for dispersal is a fundamental fitness component of plant pathogens. Characterization of plant pathogen dispersal is important for understanding how pathogen populations change in time and space. We devised a systematic approach to measure and analyze rain splash-driven dispersal of plant pathogens in field conditions, using the major fungal wheat pathogen Zymoseptoria tritici as a case study. We inoculated field plots of wheat ( Triticum aestivum) with two distinct Z. tritici strains. Next, we measured disease intensity as counts of fruiting bodies (pycnidia) using automated image analysis. These measurements characterized primary disease gradients, which we used to estimate effective dispersal of the pathogen population. Genotyping of reisolated pathogen strains with strain-specific PCR confirmed the conclusions drawn from phenotypic data. Consistently with controlled environment studies, we found that the characteristic scale of dispersal is tens of centimeters. We analyzed the data using a spatially explicit mathematical model that incorporates the spatial extent of the source, rather than assuming a point source, which allows for a more accurate estimation of dispersal kernels. We employed bootstrapping methods for statistical testing and adopted a two-dimensional hypotheses test based on kernel density estimation, enabling more robust inference compared with standard methods. We report the first estimates of dispersal kernels of the pathogen in field conditions. However, repeating the experiment in other environments would lead to more robust conclusions. We put forward advanced methodology that paves the way for further measurements of plant pathogen dispersal in field conditions, which can inform spatially targeted plant disease management.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Association of Simulation Training With Rates of Medical Malpractice Claims Among Obstetrician–Gynecologists
Authors: Schaffer Adam C. , Babayan Astrid , Einbinder Jonathan S. , Sato Luke , Gardner Roxane
Published: July 2021

OBJECTIVE:

To compare malpractice claim rates before and after participation in simulation training, which focused on team training during a high-acuity clinical case.

METHODS:

We performed a retrospective analysis comparing the claim rates before and after simulation training among 292 obstetrician–gynecologists, all of whom were insured by the same malpractice insurer, who attended one or more simulation training sessions from 2002 to 2019. The insurer provided malpractice claims data involving study physicians, along with durations of coverage, which we used to calculate claim rates, expressed as claims per 100 physician coverage years. We used three different time periods in our presimulation and postsimulation training claim rates comparisons: the entire study period, 2 years presimulation and postsimulation training, and 1 year presimulation and postsimulation training. Secondary outcomes included indemnity payment amounts, percent of claims paid, and injury severity.

RESULTS:

Compared with presimulation training, malpractice claim rates were significantly lower postsimulation training for the full study period (11.2 vs 5.7 claims per 100 physician coverage years; P<.001) and the 2 years presimulation and postsimulation training (9.2 vs 5.4 claims per 100 physician coverage years; P=.043). For the 1 year presimulation and postsimulation training comparison, the decrease in claim rates was nonsignificant (8.8 vs 5.3 claims per 100 physician coverage years; P=.162). Attending more than one simulation session was associated with a greater reduction in claim rates. Postsimulation claim rates for physicians who attended one, two, or three or more simulation sessions were 6.3, 2.1, and 1.3 claims per 100 physician coverage years, respectively (P<.001). Compared with presimulation training, there was no significant difference in the median or mean indemnity paid, percent of claims on which an indemnity payment was made, or median severity of injury after simulation training.

CONCLUSION:

We observed a significant reduction in malpractice claim rates after simulation training. Wider use of simulation training within obstetrics and gynecology should be considered.
Discrepancies Created by Surgeon Self-Reported Operative Time and the Effects on Procedural Relative Value Units and Reimbursement
Authors: Uppal Shitanshu , Rice Laurel W. , Spencer Ryan J.
Published: July 2021

OBJECTIVE:

To demonstrate discrepancies between operative times in the ACS NSQIP (American College of Surgeons National Surgical Quality Improvement Project) and self-reported operative time from the American Medical Association's Relative Value Scale Update Committee (RUC) and their effect on relative value units (RVU) determination.

METHODS:

This is a cross-sectional review of registry data using the ACS NSQIP 2016 Participant User File and the Centers for Medicare & Medicaid Services physician procedure time file for 2018. We analyzed total RVUs for surgeries by operative time to calculate RVU per hour and stratified by specialty. Multivariate regression analysis adjusted for patient comorbidities, age, length of stay, and ACS NSQIP mortality and morbidity probabilities. The surgeon self-reported operative times from the Centers for Medicare & Medicaid Services physician were compared with operative times recorded in the ACS NSQIP, with excess time from RUC estimates termed “overreported time.”

RESULTS:

Analysis of 901,917 surgeries revealed a wide variation in median RVU per hour between specialties. Orthopedics (14.3), neurosurgery (12.9), and general surgery (12.1) had the highest RVU per hour, whereas gynecology (10.2), plastic surgery (9.5), and otolaryngology (9) had the lowest (P<.001 for all comparisons). These results remained unchanged on multivariate regression analysis. General surgery had the highest median overreported operative time (+26 minutes) followed by neurosurgery (+23.5 minutes) and urology (+20 minutes). Overreporting of the operative time strongly correlated to higher RVU per hour (r=0.87, P=.002).

CONCLUSION:

Despite reliable electronic records, the AMA-RUC continues to use inaccurate self-reported RUC surveys for operative times. This results in discrepancies in RVU per hour (and subsequent reimbursement) across specialties and a persistent disparity for women-specific procedures in gynecology. Relative value unit levels should be based on the available objective data to eliminate these disparities.
Veno-arterial Extracorporeal Membrane Oxygenation as Bridge to Heart Transplantation: The Way Forward
Authors: Montisci Andrea , Donatelli Francesco , Cirri Silvia , Coscioni Enrico , Maiello Ciro , Napoli Claudio
Published: July 2021

Advanced heart failure (HF) represents a public health priority due to the increase of affected patients and the meaningful mortality. Durable mechanical circulatory support (MCS) and heart transplantation (HTx) are unique therapies for end-stage HF (ESHF), with positive early and long-term outcomes. The patients who underwent HTx have a 1-y survival of 91% and a median survival of 12–13 y, whereas the median survival of ESHF is <12 mo. Short-term MCS with veno-arterial extracorporeal membrane oxygenation (VA ECMO) can be used as a bridge to transplantation strategy. Patients bridged with VA ECMO have significantly lower survival in comparison with non-MCS bridged and left ventricular assist device-bridged patients. VA ECMO represents an effective, and sometimes unique, system to obtain rapid hemodynamic stabilization, but possible negative effects on patients’ outcomes after HTx must be considered. Here, we discuss the use of VA ECMO as bridge to transplantation.
Improved detection of flaviviruses in Australian mosquito populations via replicative intermediates
Authors: O'Brien Caitlin A. , Harrison Jessica J. , Colmant Agathe M. G. , Traves Renee J. , Paramitha Devina , Hall-Mendelin Sonja , Bielefeldt-Ohmann Helle , Vet Laura J. , Piyasena Thisun B. H. , Newton Natalee D. , Yam Alice W. , Hobson-Peters Jody , Hall Roy A.
Published: July 2021

Mosquito-borne flaviviruses are significant contributors to the arboviral disease burdens both in Australia and globally. While routine arbovirus surveillance remains a vital exercise to identify known flaviviruses in mosquito populations, novel or divergent and emerging species can be missed by these traditional methods. The MAVRIC (monoclonal antibodies to viral RNA intermediates in cells) system is an ELISA-based method for broad-spectrum isolation of positive-sense and double-stranded RNA (dsRNA) viruses based on detection of dsRNA in infected cells. While the MAVRIC ELISA has successfully been used to detect known and novel flaviviruses in Australian mosquitoes, we previously reported that dsRNA could not be detected in dengue virus-infected cells using this method. In this study we identified additional flaviviruses which evade detection of dsRNA by the MAVRIC ELISA. Utilising chimeric flaviviruses we demonstrated that this outcome may be dictated by the non-structural proteins and/or untranslated regions of the flaviviral genome. In addition, we report a modified fixation method that enables improved detection of flavivirus dsRNA and inactivation of non-enveloped viruses from mosquito populations using the MAVRIC system. This study demonstrates the utility of anti-dsRNA monoclonal antibodies for identifying viral replication in insect and vertebrate cell systems and highlights a unique characteristic of flavivirus replication.
Monitoring the 5’UTR landscape reveals 5’terminal oligopyrimidine (TOP) motif switches to drive translational efficiencies
Authors: Weber Ramona , Ghoshdastider Umesh , Spies Daniel , Duré Clara , Valdivia-Francia Fabiola , Forny Merima , Ormiston Mark , Renz Peter F. , Taborsky David , Yigit Merve , Yamahachi Homare , Sendoel Ataman
Published: July 2021

Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here we use long-read sequencing to document the 5’and 3’untranslated region (UTR) isoform landscape of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5’UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. These 5’UTR isoforms with identical coding sequences either include or exclude 5’terminal oligopyrimidine (TOP) motifs and result in vastly altered translational efficiencies of the mRNA. Our findings suggest that switching between TOP and non-TOP motif-containing 5’UTR isoforms is an elegant and simple way to alter protein synthesis rates, set their sensitivity to the mTORC1-dependent nutrient-sensing pathway and direct the translational potential of an mRNA by the precise 5’UTR sequence.
Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil
Authors: Rego Natalia , Fernández-Calero Tamara , Arantes Ighor , Noya Verónica , Mir Daiana , Brandes Mariana , Zanetti Juan , Arleo Mailen , Pereira Emiliano , Possi Tania , Chappos Odhille , Bilbao Lucia , Reyes Natalia , Duquía Melissa , Victoria Matías , Techera Pía , Benítez-Galeano María José , Griffero Luciana , Méndez Mauricio , González Belén , Smircich Pablo , Colina Rodney , Alonso Cecilia , Bello Gonzalo , Spangenberg Lucía
Published: July 2021

During the first nine months of the SARS-CoV-2 pandemic, Uruguay successfully kept it under control, even when our previous studies support a recurrent viral flux across the Uruguayan-Brazilian border that sourced several local outbreaks in Uruguay. However, towards the end of 2020, a remarkable exponential growth was observed and the TETRIS strategy was lost. Here, we aimed to understand the factors that fueled SARS-CoV-2 viral dynamics during the first epidemic wave in the country. We recovered 84 whole viral genomes from patients diagnosed between November, 2020 and February, 2021 in Rocha, a sentinel eastern Uruguayan department bordering Brazil. The lineage B.1.1.28 was the most prevalent in Rocha during November-December 2020, P.2 became the dominant one during January-February 2021, while the first P.1 sequences corresponds to February, 2021. The lineage replacement process agrees with that observed in several Brazilian states, including Rio Grande do Sul (RS). We observed a one to three month delay between the appearance of P.2 and P.1 in RS and their subsequent detection in Rocha. The phylogenetic analysis detected two B.1.1.28 and one P.2 main Uruguayan SARS-CoV-2 clades, introduced from the southern and southeastern Brazilian regions into Rocha between early November and mid December, 2020. One synonymous mutation distinguishes the sequences of the main B.1.1.28 clade in Rocha from those widely distributed in RS. The minor B.1.1.28 cluster, distinguished by several mutations, harbours non-synonymous changes in the Spike protein: Q675H and Q677H, so far not concurrently reported. The convergent appearance of S:Q677H in different viral lineages and its proximity to the S1/S2 cleavage site raise concerns about its functional relevance. The observed S:E484K-VOI P.2 partial replacement of previously circulating lineages in Rocha might have increased transmissibility as suggested by the significant decrease in Ct values. Our study emphasizes the impact of Brazilian SARS-CoV-2 epidemics in Uruguay and the need of reinforcing real-time genomic surveillance on specific Uruguayan border locations, as one of the key elements for achieving long-term COVID-19 epidemic control.
Early management of severe COVID-19 coagulopathy should be guided by TEG®, microclot and platelet mapping
Authors: Laubscher Gert Jacobus , Lourens Petrus Johannes , Venter Chantelle , Kell Douglas B , Pretorius Etheresia
Published: July 2021

An important component of severe COVID-19 disease is virus-induced endothelilitis. This leads to disruption of normal endothelial function, initiating a state of failing normal clotting physiology. Massively increased levels of von Willebrand Factor (VWF) lead to overwhelming platelet activation, as well as activation of the enzymatic (intrinsic) clotting pathway. In addition, there is an impaired fibrinolysis, caused by, amongst others, increased levels of alpha-(2) antiplasmin. The end result is hypercoagulation [proven by thromboelastography®(TEG®)] and reduced fibrinolysis, inevitably leading to a difficult-to-overcome hypercoagulated physiological state. Platelets in circulation also plays a significant role in clot formation, but themselves may also drive hypercoagulation when they are overactivated due to the interactions of their receptors with the endothelium, immune cells or circulating inflammatory molecules. From the literature it is clear that the role of platelets in severely ill COVID-19 patients has been markedly underestimated or even ignored. We here highlight the value of early management of severe COVID-19 coagulopathy as guided by TEG®, microclot and platelet mapping. We also argue that the failure of clinical trials, where the efficacy of prophylactic versus therapeutic clexane (low molecular weight heparin (LMWH)) were not always successful, might be because the significant role of platelet activation was not taken into account during the planning of the trial. We conclude that, because of the overwhelming alteration of clotting, the outcome of any trial evaluating an any single anticoagulant, including thrombolytic, would be negative. Here we suggest the use of the degree of platelet dysfunction and presence of microclots in circulation, together with TEG®, should be used as a guideline for disease severity. A multi-pronged approach, guided by TEG®and platelet mapping, would be required to maintain normal clotting physiology in severe COVID-19 disease.
A Pilot Study of High-Intensity Interval Training in Older Adults with Treatment Naïve Chronic Lymphocytic Leukemia
Authors: MacDonald Grace , Sitlinger Andrea , Deal Michael A. , Hanson Erik D. , Ferraro Stephanie , Pieper Carl F. , Weinberg J. Brice , Brander Danielle M. , Bartlett David B.
Published: July 2021

Chronic lymphocytic leukemia (CLL) is the most common leukemia in the USA, affecting predominantly older adults. CLL is characterized by low physical fitness, reduced immunity, and increased risk of secondary malignancies and infections. One approach to improving physical fitness and immune functions is participation in a structured exercise program. The aims of this pilot study were to determine the feasibility and outcomes of 12-weeks of high-intensity interval training (HIIT) combined with muscle endurance-based resistance training on older adults with treatment naïve CLL. We enrolled eighteen participants with CLL aged 64.9 (9.1) years and assigned them to groups depending on distance lived from our fitness center. Ten participants (4M/6F) completed HIIT and six participants (4M/2F) completed a non-exercising control group (Controls). HIIT consisted of three 30-minute treadmill sessions/week plus two concurrent 30-minute strength training sessions/week. We confirmed feasibility if >70% of HIIT participants completed >75% of prescribed sessions and prescribed minutes, and if >80% of high-intensity intervals were at a heart rate corresponding to 80% of aerobic capacity [139 (19) bpm]. Other outcomes included aerobic capacity, muscle strength and endurance, and natural killer (NK) cell recognition and killing of tumor cells. Results are presented as Hedge’s G effect sizes (g), with 0.2, 0.5 and 0.8 representing small, medium and large effects, respectively. Feasibility was achieved, with HIIT completing 5.0 (0.2) sessions/week and 99 (3.6)% of prescribed minutes/week at 142 (19)bpm. Following HIIT, leg strength (g=2.52), chest strength (g=1.15) and seated row strength (g=3.07) were 35.4%, 56.1% and 39.5% higher, respectively, while aerobic capacity was 3.8% lower (g=0.49) than changes for Controls. Similarly, following HIIT, in vitro NK-cell cytolytic activity against the K562 cell line (g=1.43), OSU-CLL cell line (g=0.95), and autologous B-cells (g=1.30) were 20.3%, 3.0% and 14.6% higher, respectively, than changes for Controls. We demonstrate that 12-weeks of HIIT combined with muscle endurance-based resistance training is feasible in older adults with untreated CLL and that HIIT has a large effect on muscle strength and important components of immune function.
The genetic architecture of Alzheimer disease risk in the Ohio and Indiana Amish
Authors: Osterman Michael D. , Song Yeunjoo E. , Adams Larry D. , Laux Renee A. , Caywood Laura J. , Prough Michael B. , Clouse Jason E. , Herington Sharlene D. , Slifer Susan H. , Lynn Audrey , Fuzzell M. Denise , Fuzzell Sarada L. , Hochstetler Sherri D. , Miskimen Kristy , Main Leighanne R. , Dorfsman Daniel A. , Ogrocki Paula , Lerner Alan J. , Ramos Jairo , Vance Jeffery M. , Cuccaro Michael L. , Scott William K. , Pericak-Vance Margaret A. , Haines Jonathan L.
Published: July 2021

Alzheimer disease (AD) is the most common type of dementia and is currently estimated to affect 6.2 million Americans. It ranks as the sixth leading cause of death in the United States and the proportion of deaths due to AD has been increasing since the year 2000 while the proportion of many other leading causes of deaths have decreased or remained constant. The risk for AD is multifactorial, including genetic and environmental risk factors. ThoughAPOEremains the largest genetic risk factor for AD, more than 26 other loci have been associated with AD risk. Here, we recruited from a population of Amish adults from Ohio and Indiana to investigate AD risk and protective genetic effects. With slightly lower incidence and later age of onset, it is thought that the Amish may hold protective genetic variants for AD. As a founder population that typically practices endogamy, variants that are rare in the general population may be at higher frequency in the Amish population. We characterized the genetic architecture of AD risk in the Amish and compared this to a non-Amish population, elucidating the lower relative importance ofAPOEand differing genetic architecture of the Amish compared to a general European ancestry population.
Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
Authors: Mohapatra Jugal , Tashiro Kyuto , Beckner Ryan L. , Sierra Jorge , Kilgore Jessica A. , Williams Noelle S. , Liszczak Glen
Published: July 2021

Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto full-length proteins with precise control over chain length and modification site. A series of semi-synthetic ADP-ribosylated histone proteins are prepared which demonstrate that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. Importantly, we found ALC1 selectively remodels ‘activated’ substrates within heterogeneous nucleosome populations and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a method that is broadly applicable to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.
Neural activity tracking identity and confidence in social information
Authors: Trudel Nadescha , Rushworth Matthew FS , Wittmann Marco K
Published: July 2021

Humans learn about the environment either directly by interacting with it or indirectly by seeking information about it from social sources such as conspecifics. The degree of confidence in the information obtained through either route should determine the impact that it has on adapting and changing behaviour. We examined whether and how behavioural and neural computations differ during non-social learning as opposed to learning from social sources. Trial-wise confidence judgments about non-social and social information sources offered a window into this learning process. Despite matching exactly the statistical features of social and non-social conditions, confidence judgments were more accurate and less changeable when they were made about social as opposed to non-social information sources. In addition to subjective reports of confidence, differences were also apparent in the Bayesian estimates of participants’ subjective beliefs. Univariate activity in dorsomedial prefrontal cortex (dmPFC) and posterior temporo-parietal junction (pTPJ) more closely tracked confidence about social as opposed to non-social information sources. In addition, the multivariate patterns of activity in the same areas encoded identities of social information sources compared to non-social information sources.
A cell type-specific multiomics uncovers a guard cell-specific RAF15-SnRK2.6/OST1 kinase cascade
Authors: Wang Hongliang , Wang Yubei , Li Rongxia , Ren Weiwei , Sang Tian , Zhao Bing , Wang Xiao , Zhang Xuebin , Dai Shaojun , Hsu Chuan-Chih , Song Chun-Peng , Wang Pengcheng
Published: July 2021

Multicellular organisms such as plants contain different cell types with specialized functions. Analyzing the characteristics of each cell type reveals specific cell functions and enhances understanding of organization and function at the organismal level. Here we report a highly-sensitive and efficient cell type-specific multiomics pipeline, combining simplified flow cytometry-based cell sorting for fluorescent protoplasts and optimized nanoscale proteomics and metabolomics methods, which allow in-depth analysis of the proteomes and metabolomes of a particular cell type. Using this method, we quantitatively compared the proteomes and metabolomes of guard cells and mesophyll cells and revealed that the enrichment of signal transduction-related proteins enables guard cells to respond rapidly to various environmental stimuli. We uncovered a guard cell-specific kinase cascade whereby RAF15 and OST1 mediate ABA-induced stomatal closure. This pipeline can be applied to various cell types in plant or non-plant systems to learn how cells function in highly organized multicellular organisms.
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction
Authors: Robert Philippe A. , Akbar Rahmad , Frank Robert , Pavlović Milena , Widrich Michael , Snapkov Igor , Slabodkin Andrei , Chernigovskaya Maria , Scheffer Lonneke , Smorodina Eva , Rawat Puneet , Mehta Brij Bhushan , Vu Mai Ha , Mathisen Ingvild Frøberg , Prósz Aurél , Abram Krzysztof , Olar Alex , Miho Enkelejda , Haug Dag Trygve Tryslew , Lund-Johansen Fridtjof , Hochreiter Sepp , Haff Ingrid Hobæk , Klambauer Günter , Sandve Geir Kjetil , Greiff Victor
Published: July 2021

Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: The lack of a unified ML formalization of immunological antibody specificity prediction problems and the unavailability of large-scale synthetic benchmarking datasets of real-world relevance. Here, we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based 3D-antibody-antigen binding structures with ground-truth access to conformational paratope, epitope, and affinity. We formalized common immunological antibody specificity prediction problems as ML tasks and confirmed that for both sequence and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework thus enables real-world relevant development and benchmarking of ML strategies for biotherapeutics design.

Graphical abstract

The software framework Absolut! enables (A,B) the generation of virtually arbitrarily large numbers of synthetic 3D-antibody-antigen structures, (C,D) the formalization of antibody specificity as machine learning (ML) tasks as well as the exploration of ML strategies for real-world antibody-antigen binding or paratope-epitope prediction.

Highlights

Software framework Absolut! to generate an arbitrarily large number of synthetic 3D-antibody-antigen structures that contain biological layers of antibody-antigen binding complexity that render ML predictions challenging

Immunological antibody specificity prediction problems formalized as machine learning tasks for which the in silico complexes are immediately usable as benchmark datasets

Exploration of machine learning prediction accuracy as a function of architecture, dataset size, choice of negatives, and sequence-structure encoding

Relative ML performance learnt on Absolut! datasets transfers to experimental datasets
Bcl-3 suppresses Th9 differentiation by regulating glutamine utilization
Authors: Tang Wanhu , Wang Hongshan , Murphy Philip M. , Siebenlist Ulrich
Published: July 2021

Bcl-3 is an atypical member of the IκB protein family that plays important and diverse roles in both innate and adaptive immunity, including Th17-dependent autoimmunity models in mice. When naïve mouse splenic CD4+ T cells were cultured under Th17 conditions in vitro, we unexpectedly found that the most highly differentially expressed gene between wild type and Bcl-3-deficient (KO) Th17 cells encoded the cytokine IL-9. We therefore investigated the role of Bcl-3 in Th9 cell differentiation. When naïve CD4+ T cells were cultured under Th9-polarizing conditions in vitro, the extent of Th9 differentiation observed in wild type cells was increased in Bcl-3 KO cells and conversely was decreased in cells overexpressing Bcl-3. The suppressive effect of Bcl-3 on Th9 differentiation was cell-autonomous, and NF-κB inhibitors abolished increased Th9 differentiation in Bcl-3 KO cells. Consistent with this, in the Th9 transfer model of OVA-induced allergic airway inflammation, mice receiving Bcl-3 KO cells had greater immune cell infiltration in the lung than mice receiving wild type cells.

Mechanistically, unsupervised transcriptomic analysis revealed differentially expressed genes in KO cells, including the glutamine transporter Slc1a5, which was downregulated. The functional significance of this was suggested by the ability of increasing concentrations of glutamine in the media to reduce the difference in Th9 differentiation between WT and KO cells. Our results suggest a novel role for Bcl-3 as a negative regulator of Th9 differentiation, in part by limiting glutamine accessibility through downregulation of Slc1a5.
Multi-modal locomotor costs explain sexual size but not shape dimorphism in a leaf-mimicking insect
Authors: Boisseau Romain P. , Büscher Thies H. , Klawitter Lexi J. , Gorb Stanislav N. , Emlen Douglas J. , Tobalske Bret W.
Published: July 2021

In most arthropods, adult females are larger than males, and male competition is a race to quickly locate and mate with scattered females (scramble competition polygyny). In this context, smaller males may be favored due to more efficient locomotion leading to higher mobility during mate searching while larger males may benefit from increased speed and higher survivorship. Understanding how body size affects different aspects of the locomotor performance of males is therefore essential to shed light on the evolution of this widespread mating system. Using a combination of empirical measures of flight performance and substrate adhesion, and modelling of body aerodynamics, we show that large body size impairs both flight and landing (attachment) performance in male leaf insects (Phyllium philippinicum), a species where relatively small and skinny males fly through the canopy in search of large sedentary females. Smaller males were more agile in the air, ascended more rapidly during flight, and had a lower risk of detaching from the substrates on which they walk and land. Our models revealed variation in body shape affected body lift and drag, but tradeoffs with weight meant that effects were negligible, suggesting that flight costs do not explain the evolution of strong sexual dimorphism in body shape in this species.

Graphical abstract
Autoimmunity increases susceptibility to and mortality from sepsis
Authors: Jensen Isaac J. , Jensen Samantha N. , McGonagill Patrick W. , Griffith Thomas S. , Mangalam Ashutosh K. , Badovinac Vladimir P.
Published: July 2021

Our prior publication detailing how sepsis influences subsequent development of EAE presented a conceptual advance in understanding the post-sepsis chronic immunoparalysis state (Jensen et al., 2020). However, the reverse scenario (autoimmunity prior to sepsis) defines a high-risk patient population whose susceptibility to sepsis remains poorly defined. Herein, we present a retrospective analysis of University of Iowa Hospital and Clinics patients demonstrating increased sepsis incidence among MS, relative to non-MS, patients. To interrogate how autoimmune disease influences host susceptibility to sepsis well-established murine models of MS and sepsis, EAE and CLP, respectively, were utilized. EAE, relative to non-EAE, mice were highly susceptible to sepsis-induced mortality with elevated cytokine storms. These results were further recapitulated in LPS andS. pneumoniaesepsis models. This work highlights both the relevance of identifying highly susceptible patient populations and expands the growing body of literature that host immune status at the time of septic insult is a potent mortality determinant.
Synthetic genomic reconstitution reveals principles of mammalianHoxcluster regulation
Authors: Pinglay Sudarshan , Bulajić Milica , Rahe Dylan P. , Huang Emily , Brosh Ran , German Sergei , Cadley John A. , Rieber Lila , Easo Nicole , Mahony Shaun , Maurano Matthew T. , Holt Liam J. , Mazzoni Esteban O. , Boeke Jef D.
Published: July 2021

PreciseHoxgene expression is crucial for embryonic patterning. Intra-Hoxtranscription factor binding and distal enhancer elements have emerged as the major regulatory modes controllingHoxgene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce ‘synthetic regulatory reconstitution’, a novel conceptual framework for studying gene regulation and apply it to theHoxAcluster. We synthesized and delivered variant ratHoxAclusters (130-170 kilobases each) to an ectopic location in the mouse genome. We find that aHoxAcluster lacking distal enhancers recapitulates correct patterns of chromatin remodeling and transcription in response to patterning signals, while distal enhancers are required for full transcriptional output. Synthetic regulatory reconstitution is a generalizable strategy to decipher the regulatory logic of gene expression in complex genomes.

One-Sentence Summary

Reconstitution of gene regulation using large DNA constructs unravels the regulatory logic of a developmental gene locus.
Shallow neural networks trained to detect collisions recover features of visual loom-selective neurons
Authors: Zhou Baohua , Li Zifan , Kim Sunnie S. Y. , Lafferty John , Clark Damon A.
Published: July 2021

Animals have evolved sophisticated visual circuits to solve a vital inference problem: detecting whether or not a visual signal corresponds to an object on a collision course. Such events are detected by specific circuits sensitive to visual looming, or objects increasing in size. Various computational models have been developed for these circuits, but how the collision-detection inference problem itself shapes the computational structures of these circuits remains unknown. Here, inspired by the distinctive structures of LPLC2 neurons in the visual system of Drosophila, we build an anatomically-constrained shallow neural network model and train it to identify visual signals that correspond to impending collisions. Surprisingly, the optimization arrives at two distinct, opposing solutions, only one of which matches the actual dendritic weighting of LPLC2 neurons. The LPLC2-like solutions are favored when a population of units is trained on the task, but not when units are trained in isolation. The trained model reproduces experimentally observed LPLC2 neuron responses for many stimuli, and reproduces canonical tuning of loom sensitive neurons, even though the models are never trained on neural data. These results show that LPLC2 neuron properties and tuning are predicted by optimizing an anatomically-constrained neural network to detect impending collisions.
Dual inhibition of anti-apoptotic proteins BCL-XL and MCL-1 enhances cytotoxicity of Nasopharyngeal carcinoma cells
Authors: Rahman Siti Fairus Abdul , Azlan Azali , Lo Kwok-Wai , Azzam Ghows , Mohana-Kumaran Nethia
Published: July 2021

One of the many strategies that cancer cells use to evade cell death is through upregulation of the BCL-2 anti-apoptotic proteins. Hence, these proteins have become attractive therapeutic targets. Given that different cell population rely on different anti-apoptotic proteins for survival, it is crucial to determine which proteins are important for NPC survival. Here we determined the survival requirements for the NPC cells using combination of CRISPR/Cas9 technique and pharmacological approaches. A human apoptosis RT2 Profiler PCR Array was first employed to profile the anti-apoptotic gene expressions in NPC cell lines HK-1 and C666-1. The HK-1 cells expressed all the anti-apoptotic genes (MCL-1, BFL-1, BCL-2, BCL-XL, and BCL-w). Similarly, the C666-1 cells expressed all the anti-apoptotic proteins except BFL-1 (undetectable level). Notably, both cell lines highly expressed MCL-1. Deletion of MCL-1 sensitized cells to A-1331852 suggesting that MCL-1 and BCL-XL may be important for NPC cell survival. Co-inhibition of MCL-1 and BCL-2 with MCL-1 selective inhibitor S63845 and BCL-2 selective inhibitor ABT-199 inhibited NPC cell proliferation but the effect on cell viability was more profound with co-inhibition of MCL-1 and BCL-XL with S63845 and A-1331852, implying that MCL-1 and BCL-XL are crucial for NPC cell survival. Furthermore, co-inhibition of MCL-1 and BCL-XL inhibited the growth and invasion of NPC spheroids. Deletion of BFL-1 sensitized cells to A-1331852 suggesting that BFL-1 may play a role in NPC cell survival. Taken together co-inhibition of BCL-XL and MCL-1/BFL-1 could be potential treatment strategies for NPC.
Nonstoichiometric balanced complexes: Implications on the effective deficiency of the underlying metabolic network
Authors: Langary Damoun , Küken Anika , Nikoloski Zoran
Published: July 2021

The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network’s capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state.
A single full-length VAR2CSA ectodomain variant purifies broadly neutralizing antibodies against placental malaria isolates
Authors: Doritchamou Justin Y. A. , Renn Jonathan P. , Jenkins Bethany , Fried Michal , Duffy Patrick E.
Published: July 2021

Placental malaria (PM) is a deadly syndrome most frequent and severe in first pregnancies. PM results from accumulation of Plasmodium falciparum (Pf)-infected erythrocytes (IE) that express the surface antigen VAR2CSA and bind to chondroitin sulfate A (CSA) in the placenta. Women become PM-resistant over successive pregnancies as they develop anti-adhesion and anti-VAR2CSA antibodies, supporting VAR2CSA as the leading PM-vaccine candidate. However, the first VAR2CSA subunit vaccines failed to induce broadly neutralizing antibody and it is still unclear whether naturally acquired protective antibodies target variant or conserved epitopes. This is crucial to determine whether effective vaccines will require incorporation of many or only a single VAR2CSA allele.

Here, IgG from multigravidae was sequentially purified on five full-length VAR2CSA ectodomain variants, thereby depleting IgG reactivity to each. The five VAR2CSA variants purified ∼0.7% of total IgG and yielded both strain-transcending and strain-specific reactivity to VAR2CSA and IE-surface antigen. IgG purified on the first VAR2CSA antigen displayed broad cross-reactivity to both recombinant and native VAR2CSA variants, and inhibited binding of all isolates to CSA. IgG remaining after depletion on all variants showed significantly reduced binding-inhibition activity compared to initial total IgG.

These findings demonstrate that a single VAR2CSA ectodomain variant displays neutralizing epitopes shared by multiple parasites, including maternal isolates, and suggest that a broadly effective PM-vaccine can be achieved with a limited number of VAR2CSA variants.