bluuebunny/crossref_metadata_2025 huggingface dataset:
Voxel-Based Diktiometry - Combining convolutional neural networks with voxel-based analysis and its application in diffusion tensor imaging for Parkinson’s disease
Authors: Estudillo-Romero Alfonso , Haegelen Claire , Jannin Pierre , Baxter John S.H.
Published: May 2022

Extracting population-wise information from medical images, specifically in the neurological domain, is crucial to better understanding disease processes and progression. This is frequently done in a whole-brain voxel-wise manner, in which a population of patients and healthy controls are registered to a common co-ordinate space and a statistical test is performed on the distribution of image intensities for each location. Although this method has yielded a number of scientific insights, it is further from clinical applicability as the differences are often small and altogether do not permit for a performant classifier. In this paper, we take the opposite approach of using a performant classifier, specifically a traditional convolutional neural network, and then extracting insights from it which can be applied in a population-wise manner, a method we call voxel-based diktiometry. We have applied this method to diffusion tensor imaging (DTI) analysis for Parkinson’s Disease, using the Parkinson’s Progression Markers Initiative (PPMI) database. By using the network sensitivity information, we can decompose what elements of the DTI contribute the most to the network’s performance, drawing conclusions about diffusion biomarkers for Parkinson’s disease that are based on metrics which are not readily expressed in the voxel-wise approach.
Noninvasive ventilation strategies for patients with severe or critical COVID-19: A rapid review of clinical outcomes
Authors: Kelly Shannon E. , Wells George A.
Published: May 2022

Objectives

To examine whether high flow nasal oxygen (HFNO), continuous positive airway pressure (CPAP), or noninvasive ventilation (NIV) strategies impact mortality, the need for invasive mechanical ventilation (IMV), or hospital and intensive care unit (ICU) length of stay compared to standard oxygen therapy (SOT) or each other in patients with severe or critical COVID-19 with acute hypoxemic respiratory failure.

Methods

A rapid review of randomized controlled trials (RCTs) identified through published systematic and rapid reviews supplemented with a search of bibliographic databases. RCTs were eligible if they compared HFNO, CPAP, or NIV to SOT or another ventilation strategy. Studies were screened, selected, and extracted by a single reviewer and checked by a second reviewer. We assessed risk of bias of included studies using the Cochrane ‘Risk of bias’ tool and used the grading of recommendations, assessment, development, and evaluation (GRADE) approach to judge the certainty of the evidence for mortality, need for IMV, and hospital and ICU length of stay. We sought RCT evidence for non-COVID-19 patients with acute hypoxemic respiratory failure and acute respiratory distress to inform additional comparisons and to supplement the available data for COVID-19.

Results

A total of 5 RCTs comparing ventilation strategies in patients with severe or critical COVID-19 were included. Patient and study characteristics were extracted and evidence and certainty of evidence assessments were completed for comparisons of HFNO and CPAP to standard oxygen therapy and NIV and CPAP to HFNO. An additional 22 RCTs of non-COVID-19 patients were also included and considered.

Results from meta-analysis suggest reductions in mortality and IMV with HFNO (RR mortality 0.87 (0.66-1.13), IMV 0.89 (0.77-1.03); low quality evidence) or CPAP (RR mortality 0.87 (0.64-1.18) low quality evidence, IMV 0.81 (0.67-0.98) moderate quality evidence) compared to SOT. Helmet NIV may reduce IMV (RR 0.69 (0.43-1.09)) and CPAP may reduce IMV (RR 0.69 (0.43-1.09)) and hospital (1.67 days fewer (5.43 fewer-2.09 more) or ICU length of stay (1.02 days fewer (3.97 fewer-1.93 more)) compared to HFNO (low quality evidence).

Conclusions

This rapid systematic review highlights the available evidence to support the use of noninvasive ventilation strategies including high flow nasal oxygen, noninvasive ventiltaion (e.g., BiPAP), or CPAP in hospitalized patients with severe or critical COVID-19 and acute hypoxemic respiratory failure who do not need emergent intubation. Findings based on moderate to very low certainty evidence suggest that noninvasive ventilation may be considered as an alternative to standard oxygen therapy to reduce hypoxemia and dyspnea. Additional high quality RCTs are warranted to reduce uncertainty and to fill in important knowledge gaps.
Impact of school closures and reopening on COVID-19 caseload in 6 cities of Pakistan: An Interrupted Time Series Analysis
Authors: Mueed Abdul , Ahmad Taimoor , Abdullah Mujahid , Sultan Faisal , Khan Adnan Ahmad
Published: May 2022

Schools were closed all over Pakistan on November 26, 2020 to reduce community transmission of COVID-19 and reopened between January 18 and February 1, 2021. However, these closures were associated with significant economic and social costs, prompting a review of effectiveness of school closures to reduce the spread of COVID-19 infections in a developing country like Pakistan. A single-group interrupted time series analysis (ITSA) was used to measure the impact of school closures, as well as reopening schools on daily new COVID-19 cases in 6 major cities across Pakistan: Lahore, Karachi, Islamabad, Quetta, Peshawar, and Muzaffarabad. We found that closing schools reduced COVID-19 incidence in the community by approximately a third of all cases nationwide. However, any benefits were contingent on continued closure of schools, as cases bounced back once schools reopened. School closures are associated with a clear and statistically significant reduction in COVID-19 cases by 0.07 to 0.63 cases per 100,000 population, while reopening schools is associated with a statistically significant increase. Lahore is an exception to the effect of school closures, but it too saw an increase in COVID-19 cases after schools reopened in early 2021. We show that closing schools was a viable policy option, especially before vaccines became available. However, its social and economic costs must also be considered.
Gender differences in perceived health in relation to working conditions and socio-economic status in Spain, 2014-2017
Authors: Godoy Amanda , Rojo Araceli , Delgado Luisa , Martín José J , Sánchez M. Teresa , López del Amo M. Puerto
Published: May 2022

A gender perspective was used to analyze how socio-economic status and per capita public health expenditure are associated to perceived health among the Spanish population between the years 2014 and 2017. Using multilevel methodologies (looking at year, individual, and region) and linear specification, the longitudinal microdata files from the Survey on Living Conditions were analyzed. The results point at low educational levels being a factor for worse perceived health among women, while for the same group income appears to have a protective influence. On the other hand, women are not negatively affected by unemployment, unlike men. Regional per capita public health expenditure is not associated with perceived health in either men nor women.
Access to Episodic Primary Care: A Cross-sectional Comparison of Walk-in Clinics and Urgent Primary Care Centers in British Columbia
Authors: McCracken Mary A. , Cooper Ian R. , Hamilton Michee-Ana , Klimas Jan , Lindsay Cameron , Fletcher Sarah , Price Morgan , Hedden Lindsay , McCracken Rita K.
Published: May 2022

Background

Walk-in clinics are non-hospital based primary care facilities that are designed to operate without appointments and provide increased healthcare access with extended hours. Urgent Primary Care Centres (UPCCs) were introduced to British Columbia (BC) in 2018 as an additional primary care resource that provides urgent, but not emergent care during extended hours. This study identifies publicly-reported access characteristics for episodic primary care in BC, and provides a clinic-level comparison between walk-in clinics and UPCCs.

Methodology

This cross-sectional study used publicly available data from all walk-in clinics and UPCCs in BC. A structured data collection form was used to record access characteristics from clinic websites, including business hours, weekend availability, attachment to a longitudinal family practice, and provision of virtual services.

Results

In total, 268 clinics were included in the analysis (243 walk-in clinics, 25 UPCCs). Of those, 225 walk-in clinics (92.6%) and two UPCCs (8.0%) were attached to a longitudinal family practice. Only 153 (63%) walk-in clinics offered weekend services, compared to 24 (96%) of UPCCs. Walk-in clinics offer the majority (8,968.6/ 78.4%) of their service hours between 08:00 and 17:00, Monday to Friday. UPCCs offer the majority (889.3/ 53.7%) of their service hours after 17:00.

Conclusion

Most walk-in clinics are associated with a longitudinal family practice and provide the majority of clinic services during typical business hours. More research that includes patient characteristics and care outcomes, analyzed at the clinic level, may be useful to support the optimization of episodic primary health care delivery.
Autonomic Nervous System Markers of Music-Elicited Analgesia in People with Fibromyalgia: A Double-Blind Randomized Pilot Study
Authors: Lepping Rebecca J. , McMillan Miranda L. , Chadwick Andrea L. , Mansour Zaid M. , Martin Laura E. , Gustafson Kathleen M.
Published: May 2022

Purpose

To investigate the feasibility of using music listening by adults with fibromyalgia (FM) as a potential tool for reducing pain sensitivity.

Patients and methods

We report results from a double-blind two-arm parallel randomized pilot study (NCT04059042) in 9 participants with FM. Pain tolerance and threshold were measured objectively using quantitative sensory tests; autonomic nervous system (ANS) reactivity was measured with electrocardiogram. Participants were randomized to listen to instrumental Western Classical music or a nature sound control to test whether music listening elicits greater analgesic effects over simple auditory distraction. Participants also completed separate control testing with no sound that was counterbalanced between participants.

Results

Participants were randomized 1:1 to music or nature sounds (4 Music, 5 Nature). Although the groups were not different on FM scores, the Music group had marginally worse pain summation (p=.09) and tolerance (p=.13). The Nature group had higher Anxiety scores (p<.05). Outcome measures showed a significant Group by Session interaction for pain tolerance (p<.05) revealing that the Nature group had greater pain reduction during audio compared to silence, while the Music group had no difference between sessions. No significant effects were observed for ANS testing. Within the Music group, there was a trend of vagal response increase from baseline to music listening, but it did not reach statistical significance; this pattern was not observed in the Nature group.

Conclusion

Auditory listening significantly altered pain responses. There may be greater vagal response to music versus nature sounds, however, results could be due to group differences in pain and anxiety. This line of study will help determine whether music could be prophylactic for people with FM when acute pain is expected.
How do local-level authorities engage in epidemic and pandemic preparedness activities and coordinate with higher levels of government? Survey results from 33 cities
Authors: Boyce Matthew R , Asprilla Melissa Cordoba , van Loenen Breanna , McClelland Amanda , Rojhani Ariella
Published: May 2022

The COVID-19 pandemic suggests that there are opportunities to improve preparedness for infectious disease outbreaks. While much attention has been given to understanding national-level preparedness, relatively little attention has been given to understanding preparedness at the local-level. We, therefore, aim to describe (1) how local governments were engaged in epidemic preparedness efforts before the COVID-19 pandemic and (2) how they were coordinating with authorities at higher levels of governance before COVID-19. We developed an online survey and distributed it to 50 cities around the world involved in the Partnership for Healthy Cities. The survey included several question formats including free-response, matrices, and multiple-choice questions. RACI matrices, a project management tool that helps explain coordination structures, were used to understand the level of government responsible, accountable, consulted, and informed regarding select preparedness activities. We used descriptive statistics to summarize local-level engagement in epidemic preparedness. Local health authorities from 33 cities completed the survey. Prior to the COVID-19 pandemic, 20 of the cities had completed infectious disease risk assessments, 10 completed all-hazards risk assessments, 11 completed simulation exercises, 10 completed after-action reviews, 19 developed preparedness and response plans, three reported involvement in their country’s Joint External Evaluation of the International Health Regulations, and eight cities reported involvement in the development of their countries’ National Action Plan for Health Security. RACI matrices revealed various models of epidemic preparedness, with responsibility often shared across levels, and national governments accountable for the most activities, compared to other governance levels. In conclusion, national governments maintain the largest role in epidemic and pandemic preparedness but the role of subnational and local governments is not negligible. Local-level actors engage in a variety of preparedness activities and future efforts should strive to better include these actors in preparedness as a means of bolstering local, national, and global health security.
Microphase separation of living cells
Authors: Carrère A. , d’Alessandro J. , Cochet-Escartin O. , Hesnard J. , Ghazi N. , Rivière C. , Anjard C. , Detcheverry F. , Rieu J.-P.
Published: May 2022

Self-organization of cells is central to a variety of biological systems and physical concepts of condensed matter have proven instrumental in deciphering some of their properties. Here we show that microphase separation, long studied in polymeric materials and other inert systems, has a natural counterpart in living cells. When placed below a millimetric film of liquid nutritive medium, a quasi two-dimensional, high-density population of Dictyostelium discoideum cells spontaneously assemble into compact domains. Their typical size of 100 μm is governed by a balance between competing interactions: an adhesion acting as a short-range attraction and promoting aggregation, and an effective long-range repulsion stemming from aerotaxis in near anoxic condition. Experimental data, a simple model and cell-based simulations all support this scenario. Our findings establish a generic mechanism for self-organization of living cells and highlight oxygen regulation as an emergent organizing principle for biological matter.
TriMem: A Parallelized Hybrid Monte Carlo Software for Efficient Simulations of Lipid Membranes
Authors: Siggel Marc , Kehl Sebastian , Reuter Klaus , Köfinger Jürgen , Hummer Gerhard
Published: May 2022

Lipid membranes are integral building blocks of living cells and perform a multitude of biological functions. Currently, molecular simulations of cellular-scale membrane structures at atomic resolution are nearly impossible, due to their size, complexity, and the large times-scales required. Instead, elastic membrane models are used to simulate membrane topologies and transitions between them, and to infer their properties and functions. Unfortunately, efficiently parallelized open-source simulation code to do so has been lacking. Here, we present TriMem, a parallel hybrid Monte Carlo simulation engine for triangulated lipid membranes. The kernels are efficiently coded in C++ and wrapped with Python for ease-of-use. The parallel implementation of the energy and gradient calculations and of Monte Carlo flip moves of edges in the triangulated membrane enable us to simulate also large and highly curved sub-cellular structures. For validation, we reproduce phase diagrams of vesicles with varying surface-to-volume ratios and area difference. The software can tackle a range of membrane remodelling processes on sub-cellular and cellular scales. Additionally, extensive documentation make the software accessible to the broad biophysics and computational cell biology communities.
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences
Authors: Guez Jérémy , Achaz Guillaume , Bienvenu François , Cury Jean , Toupance Bruno , Heyer Évelyne , Jay Flora , Austerlitz Frédéric
Published: May 2022

Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of children’s survival through allocare from uncle and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity through time under CTRS. We show that CTRS has a double impact on population genetics: (1) effective population size decreases when CTRS starts, mimicking a population contraction, and increases back to its original value when CTRS stops; (2) coalescent trees topologies are distorted under CTRS, with higher imbalance and higher number of polytomies. Under long-lasting CTRS, effective population size stabilises but the distortion of tree topology remains, which yields U-shaped Site Frequency Spectra (SFS) under constant population size. We show that this CTRS’ impact yields a bias in SFS-based demographic inference. Considering that CTRS was detected in numerous human and animal populations worldwide, one should be cautious that inferring population past histories from genomic data can be biased by this cultural process.
The central autonomic system revisited – convergent evidence for a regulatory role of the insular and midcingulate cortex from neuroimaging meta-analyses
Authors: Ferraro Stefania , Klugah-Brown Benjamin , Tench Christopher R , Chepngetich Bore Mercy , Nigri Anna , Demichelis Greta , Bruzzone Maria Grazia , Palermo Sara , Zhao Weihua , Yao Shuxia , Jiang Xi , Kendrick Keith M , Becker Benjamin
Published: May 2022

The autonomic nervous system regulates dynamic body adaptations to internal and external environment changes. Capitalizing on two different algorithms (Analysis of Brain Coordinates and GingerALE) that differ in empirical assumptions, we scrutinized the meta-analytic convergence of human neuroimaging studies investigating the neural basis of peripheral autonomic signal processing. Among the selected studies, we identified 42 records reporting 44 different experiments and testing 792 healthy individuals.

The results of the two different algorithms converge in identifying the bilateral dorsal anterior insula and midcingulate cortex as the critical areas of the central autonomic system (CAN). However, whereas the bilateral dorsal anterior insula appears to be involved in processing autonomic nervous system signals regardless of task type, activity in the midcingulate cortex appears to be primarily engaged in processing autonomic signals during cognitive tasks and task-free conditions. Applying an unbiased approach, we were able to identify a single functionally condition-independent circuit that supports CAN activity. Although partially overlapping with the salience network, this functional circuit includes, in addition to the bilateral insular cortex and midcingulate cortex, the bilateral inferior parietal lobules and small clusters in the bilateral middle frontal gyrus. Our results do not support the hypothesis of divergent pathways for the sympathetic and parasympathetic systems or a robust involvement of the default mode network, particularly during parasympathetic activity. However, these results may be due to the relatively low number of studies investigating the parasympathetic system (12%), making our results more consistent with the central processing network of sympathetic activity.

Remarkably, the critical regions of the CAN observed in this meta-analysis are among the most reported co-activated areas in neuroimaging studies and have been repeatedly shown as being dysregulated across different mental and neurological disorders. This suggests that the central dynamic interaction maintaining bodily homeostasis reported in several brain imaging studies may be associated with increased autonomic nervous system engagement and that disruptions in this interplay may underpin unspecific pathological symptoms across mental and neurological disorders.
Chimeric 3D-gastruloids – a versatile tool for studies of mammalian peri-gastrulation development
Authors: Wehmeyer Alexandra E. , Schüle Katrin M. , Conrad Alexandra , Schröder Chiara M. , Probst Simone , Arnold Sebastian J.
Published: May 2022

Stem cell-derived 3D-gastruloids show a remarkable capacity of self-organisation and recapitulate many aspects of gastrulation stage mammalian development. Gastruloids can be rapidly generated and offer several experimental advantages, such as scalability, observability, and accessibility for manipulation. Here, we present approaches to further expand the experimental potency of murine 3D-gastruloids by utilizing functional genetics in mouse embryonic stem cells (mESCs) to generate chimeric gastruloids. In chimeric gastruloids fluorescently labelled cells of different genotypes harbouring inducible gene-expression, or loss-of-function alleles, are combined with wildtype cells. We showcase this experimental approach in chimeric gastruloids of mESCs carrying homozygous deletions of the Tbx transcription factorsBrachyury, or inducible expression ofEomes. Resulting chimeric gastruloids recapitulate reportedEomesandBrachyuryfunctions, such as instructing cardiac fate and promoting posterior axial extension, respectively. Additionally, chimeric gastruloids revealed previously unrecognized phenotypes such as tissue sorting preference ofBrachyury-deficient cells to endoderm, and cell non-autonomous effects ofBrachyury-deficiency onWnt3a-patterning along the embryonic axis, demonstrating some of the advantages of chimeric gastruloids as efficient tool for studies of mammalian gastrulation.
Spinosaurusis not an aquatic dinosaur
Authors: Sereno Paul C. , Myhrvold Nathan , Henderson Donald M. , Fish Frank E. , Vidal Daniel , Baumgart Stephanie L. , Keillor Tyler M. , Formoso Kiersten K. , Conroy Lauren L.
Published: May 2022

A predominantly fish-eating diet was envisioned for the sail-backed theropod dinosaur,Spinosaurus aegyptiacus, when its elongate jaws with subconical teeth were unearthed a century ago in Egypt. Recent discovery of the high-spined tail of that skeleton, however, led to a bolder conjecture, thatS. aegyptiacuswas the first fully aquatic dinosaur. The ‘aquatic hypothesis’ posits thatS. aegyptiacuswas a slow quadruped on land but a capable pursuit predator in coastal waters, powered by an expanded tail. We test these functional claims with skeletal and flesh models ofS. aegyptiacus. We assembled a CT-based skeletal reconstruction based on the fossils, to which we added internal air and muscle to create a posable flesh model. That model shows that on landS. aegyptiacuswas bipedal and in deep water was an unstable, slow surface swimmer (<1m/s) too buoyant to dive. Living reptiles with similar spine-supported sails over trunk and tail in living reptiles are used for display rather than aquatic propulsion, and nearly all extant secondary swimmers have reduced limbs and fleshy tail flukes. New fossils also show thatSpinosaurusranged far inland. Two stages are clarified in the evolution ofSpinosaurus, which is best understood as a semiaquatic bipedal ambush piscivore that frequented the margins of coastal and inland waterways.
TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development
Authors: Feng Jifan , Han Xia , Yuan Yuan , Cho Courtney Kyeong , Janečková Eva , Guo Tingwei , Pareek Siddhika , Bi Jing , Jing Junjun , Zhang Mingyi , Ho Thach-Vu , Chai Yang
Published: May 2022

The communication between myogenic cells and their surrounding connective tissues is indispensable for muscle morphogenesis. During late embryonic development in mice, myogenic progenitors migrate to discrete sites to form individual muscles. The detailed mechanism of this process remains unclear. Using levator veli palatini (LVP) development as a model, we systematically investigated how a distinct connective tissue subpopulation, perimysial fibroblasts, communcates with myogenic cells to regulate mouse pharyngeal myogenesis. Using single-cell RNAseq data analysis, we identified that TGF-β signaling is a key regulator for the perimysial fibroblasts. Loss of TGF-β signaling led to defects in perimysial fibroblasts and subsequently muscle formation in Osr2-Cre;Alk5fl/fl mice. In particular, a perimysial fibroblast-specific regulator, Creb5, interacts with TGF-β signaling to enable specific activation of perimysial fibroblast-derived signals such as Fgf18. Moreover, Fgf18 supports pharyngeal muscle development in vivo and its exogenous expression can partially rescue myogenic cell numbers in Osr2-Cre;Alk5fl/fl samples, illustrating that TGF-β-regulated Fgf18 signaling is required for LVP development. Collectively, our findings revealed the mechanism by which TGF-β signaling achieves its specificity in defining the perimysial-to-myogenic signals for pharyngeal myogenesis.
Antiviral activity of the hemolymph ofPodalia sp and M. albicolis(Lepidoptera: Megalopigydae)
Authors: Carvalho N.D. , Curti S.P. , Oliveira M.I. , Rofatto H.K. , Figueiredo C.A. , Senna de Villar K , Magnelli R.F. , Mendonça R.Z.
Published: May 2022

Potent antiviral activity against measles, influenza, picornavirus and herpes simplex viruses was observed in the hemolymph ofPodalia spandM. Albicolis(Lepidoptera: Megalopigydae). The antiviral proteins responsible for this activity were isolated by gel filtration chromatography using a gel filtration column system (Superdex 75) and further fractionated using a Resource-Q ion exchange column system. Experiments with the semi-purified protein led to a 128-fold reduction in picornavirus production, 64-fold reduction in measles virus production and a 32-fold reduction in influenza virus replication. qPCR showed a significantly lower level of herpes virus transcription. In addition no citotoxicity and genotoxicity effect was observed for Vero cells, suggesting a very interesting potential antiviral activity.
Insulin sensitivity is preserved in mice made obese by feeding a high starch diet
Authors: Brandon Amanda E , Small Lewin , Nguyen Tuong-Vi , Suryana Eurwin , Gong Henry , Yassmin Christian , Hancock Sarah E , Pulpitel Tamara , Stonehouse Sophie , Prescott Leteisha , Kebede Melkam A , Yau Belinda , Quek Lake-Ee , Kowalski Greg M , Bruce Clinton R , Turner Nigel , Cooney Gregory J
Published: May 2022

Obesity is generally associated with insulin resistance in liver and muscle and increased risk of developing type 2 diabetes, however there is a population of obese people that remain insulin sensitive. Similarly, recent work suggests that mice fed high carbohydrate diets can become obese without apparent glucose intolerance. To investigate this phenomenon further, we fed mice either a high fat (Hi-F) or high starch (Hi-ST) diet and measured adiposity, glucose tolerance, insulin sensitivity and tissue lipids compared to control mice fed a standard laboratory chow. Both Hi-ST and Hi-F mice accumulated a similar amount of fat and tissue triglyceride compared to chow-fed mice. However while Hi-F diet mice developed glucose intolerance as well as liver and muscle insulin resistance (assessed via euglycemic/hyperinsulinemic clamp), obese Hi-ST mice maintained glucose tolerance and insulin action similar to lean, chow-fed controls. This preservation of insulin action despite obesity in Hi-ST mice was associated with differences in de novo lipogenesis and levels of C22:0 ceramide in liver and C18:0 ceramide in muscle. This indicates that dietary manipulation can influence insulin action independently of the level of adiposity and that the presence of specific ceramide species correlate with these differences.
Microenvironmental Ammonia Enhances T cell Exhaustion in Colorectal Cancer
Authors: Bell Hannah N. , Huber Amanda K. , Singhal Rashi , Rebernick Ryan J. , Kumar Roshan , Das Nupur K. , Kerk Samuel A. , Sajjakulnukit Peter , Solanki Sumeet , James Jadyn G. , Kim Donghwan , Zhang Li , El-derany Marwa O. , Frankel Timothy L. , Győrffy Balázs , Fearon Eric R. , di Magliano Marina Pasca , Gonzalez Frank J. , Banerjee Ruma , Lyssiotis Costas A. , Green Michael , Shah Yatrik M.
Published: May 2022

Effective therapies are lacking for patients with advanced colorectal cancer (CRC). The CRC tumor microenvironment has elevated metabolic waste products due to altered metabolism and proximity to the microbiota. The role of metabolite waste in tumor development, progression, and treatment resistance is unclear. We generated an autochthonous metastatic mouse model of CRC and unbiased multi-omic analyses in this model reveals a robust accumulation of tumoral ammonia. The high ammonia levels induce T cell metabolic reprogramming, increase exhaustion and decrease proliferation. CRC patients have increased serum ammonia, and our ammonia-related gene signature correlates with altered T cell response, adverse patient outcomes, and lack of response to immune checkpoint blockade. We demonstrate that enhancing ammonia clearance reactivates T cells, decreases tumor growth, and extends survival. Moreover, decreasing tumor-associated ammonia enhances anti-PD-L1 efficacy. Our findings indicate that ammonia detoxification can reactivate T cells, highlighting a new approach to enhance the efficacy of immunotherapies.

Statement of Significance

We demonstrate that ammonia accumulates in the microenvironment of colorectal cancer. Ammonia alters T-cells redox singling leading to a decrease in T cell proliferation and an increase in T cell exhaustion. Enhancing ammonia clearance reduces tumor size, increases survival, and increases the efficacy to immunotherapies.
Intraprocedural endothelial cell seeding of arterial stents via biotin/avidin targeting mitigates in-stent restenosis
Authors: Alferiev Ivan S , Hooshdaran Bahman , Pressly Benjamin B , Stachelek Stanley J , Zoltick Philip W. , Chorny Michael , Levy Robert J , Fishbein Ilia
Published: May 2022

Impaired endothelialization of endovascular stents has been established as a major cause of in-stent restenosis and late stent thrombosis[1]. Attempts to enhance endothelialization of inner stent surfaces by pre-seeding the stents with endothelial cells in vitro prior to implantation are compromised by cell destruction during high-pressure stent deployment. Herein, we report on the novel stent endothelialization strategy of post-deployment seeding of biotin-modified endothelial cells to avidin-functionalized stents. Acquisition of an avidin monolayer on the stent surface was achieved by consecutive treatments of bare metal stents (BMS) with polyallylamine bisphosphonate, an amine-reactive biotinylation reagent and avidin. Biotin-modified endothelial cells retain growth characteristics of normal endothelium and can express reporter transgenes. Under physiological shear conditions, a 50-fold higher number of recirculating biotinylated cells attached to the avidin-modified metal surfaces compared to bare metal counterparts. Delivery of biotinylated endothelial cells to the carotid arterial segment proximal to the implanted avidin-modified stent in rats results in immediate cell binding to the stent struts and is associated with a 30% reduction of in-stent restenosis in comparison with BMS.
Color-biased regions in the ventral visual pathway are food-selective
Authors: Pennock Ian Morgan Leo , Racey Chris , Allen Emily , Wu Yihan , Naselaris Thomas , Kay Kendrick , Franklin Anna , Bosten Jenny
Published: May 2022

The ventral visual pathway is well known to be involved in recognizing and categorizing objects (Kanwisher and Dilks, 2013). Three color-biased areas have also been found between face and place selective areas in the ventral visual pathway (Lafer-Sousa et al., 2016). To understand the function of these color-biased areas in a region known for object recognition, we analyzed the Natural Scenes Dataset (NSD; Allen et al., 2022), a large 7T fMRI dataset from 8 participants who viewed up to 30,000 trials of images of colored natural scenes. In a whole-brain analysis, we correlated the average color saturation of the images and the voxel responses, revealing color-biased areas that diverge into two streams in the ventral visual pathway, beginning in V4 and extending medially and laterally of the Fusiform Face Area in both hemispheres. We drew regions of interest (ROIs) for the two streams and found that the images for each ROI that evoked the largest responses had certain characteristics: They contained food, contained circular objects, had higher color saturation, contained warmer hues, and had more luminance entropy. A multiple linear regression showed that the presence of food in images was the strongest predictor of voxel responses in the medial and lateral color-biased regions for all eight participants, but that color saturation also contributed independently to voxel responses. Our results show that these areas are food-selective and color biased. We suggest that these streams might be involved in using color to recognize and judge the properties of food.
In-silico design and assessment of OprD based multi-epitope vaccine against Acinetobacter baumannii
Authors: Khalid Kashaf , Andleeb Saadia
Published: May 2022

Gram-negative, opportunist pathogen Acinetobacter baumannii is notorious for causing a plethora of nosocomial infections predominantly respiratory diseases and blood-stream infections. Due to resistance development towards last-resort antibiotics, its treatment is becoming increasingly difficult. Despite numerous therapeutic developments, no vaccine is available against this ubiquitous pathogen. It is therefore apropos to formulate a rational vaccine plan to get rid of the super-bug. Considering the importance of Outer Membrane Porin D (OprD) as a potential vaccine candidate, we methodically combined the most persistent epitopes present in the A. baumannii strains with the help of different immunoinformatic approaches to envisage a systematic multi-epitope vaccine. The proposed vaccine contains highly immunogenic stretches of linear B-cells, cytotoxic T lymphocyte epitopes, and helper T lymphocyte epitopes of outer membrane porin OprD. The finalized epitopes proved to be significant as they are conserved in A. baumannii strains. The final 3D structure of the construct was projected, refined, and verified by employing several in silico approaches. Apt binding of the protein and adjuvant with the TLR4 suggested significantly high immunogenic potential of our designed vaccine. MD simulations showed highly stable composition of the protein. Immune simulations disclosed a prominent increase in the levels of the immune response. The proposed vaccine model is proposed to be thermostable, immunogenic, water-soluble, and non-allergenic. However, this study is purely computational and needs to be validated by follow-up wet laboratory studies to confirm the safety and immunogenicity of our multi-epitope vaccine.
The Dct-/- mouse model to unravel retinogenesis misregulation in patients with albinism
Authors: Tingaud-Sequeira Angèle , Mercier Elina , Michaud Vincent , Pinson Benoît , Gazova Ivet , Gontier Etienne , Decoeur Fanny , McKie Lisa , Jackson Ian J. , Arveiler Benoît , Javerzat Sophie
Published: May 2022

We have recently identified DCT encoding dopachrome tautomerase (DCT) as the 8th gene for oculocutaneous albinism (OCA). Patients with loss of function of DCT suffer from eye hypopigmentation and retinal dystrophy. Here we investigate the eye phenotype in Dct-/- mice. We show that their retinal pigmented epithelium (RPE) is severely hypopigmented from early stages contrasting with the darker melanocytic tissues. Multimodal imaging reveals specific RPE cellular defects. Melanosomes are fewer with correct subcellular localization but disrupted melanisation. RPE cell size is globally increased and heterogeneous. P-cadherin labeling of Dct-/- newborn RPE reveals a defect in adherens junctions similar to what has been described in tyrosinase-deficient Tyrc/c embryos. The first intermediate of melanin biosynthesis, dihydroxyphenylalanine (L-Dopa), which is thought to control retinogenesis, is detected in substantial yet significantly reduced amounts in Dct-/- postnatal mouse eyecups. L-Dopa synthesis in the RPE alone remains to be evaluated during the critical period of retinogenesis. The Dct-/- mouse should prove useful in understanding the molecular regulation of retinal development and aging of the hypopigmented eye. This may guide therapeutic strategies to prevent vision deficits in patients with albinism.
Store-Operated Ca2+ Channels Mediate Microdomain Ca2+ Signals and Amplify Gq-Coupled Ca2+ Elevations in Capillary Pericytes
Authors: Phillips Braxton , Clark Jenna , Martineau Éric , Rungta Ravi L.
Published: May 2022

Pericytes are multifunctional cells of the vasculature that are vital to brain homeostasis, yet many of their fundamental physiological properties remain unexplored. Ca2+ is a ubiquitous second messenger across cell-types, where it mediates diverse functions such as contractility and gene transcription. It is therefore important to understand the cellular mechanisms underlying Ca2+ signalling in capillary pericytes. Here, we performed pharmacological and ion substitution experiments to investigate the mechanisms underlying pericyte Ca2+ signaling in acute cortical brain slices of PDGFRβ-GCaMP6f mice. We report that in mid-capillary bed pericytes (≥ 4th branch order), spontaneous microdomain Ca2+ signals are dependent on extracellular Ca2+, but largely independent of depolarization, L- and T-type voltage-gated calcium channels (VGCCs), and TRPC3/6 channels. In contrast, these microdomain signals were inhibited by multiple Orai channel blockers, including the specific antagonist GSK-7975A. Furthermore, capillary pericytes exhibited classical store operated calcium entry (SOCE) following store depletion that was sensitive to GSK-7975A and required for amplification of intracellular Ca2+ increases evoked by the vasoconstrictor endothelin-1. These results suggest that Orai SOCE mediates microdomain Ca2+ signals at rest and amplifies Gq-GPCR coupled Ca2+ elevations in capillary pericytes. Thus, SOCE is a major regulator of pericyte Ca2+ and a target for manipulating their function in health and disease.
Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities
Authors: Berckx Fede , Van Nguyen Thanh , Hilker Rolf , Wibberg Daniel , Battenberg Kai , Kalinowski Jörn , Berry Alison , Pawlowski Katharina
Published: May 2022

Frankia cluster-2 are diazotrophs that engage in root nodule symbiosis with host plants of the Cucurbitales and the Rosales. They are rarely found in the soil in the absence of their hosts. Previous studies have shown that an assimilated nitrogen source, presumable arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), but not in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported by cluster-2 strains, and which nitrogen source would then be exported to C. thyrsiflorus, gene expression levels, metabolite profiles and enzyme activities were analysed.

We found that the export of assimilated nitrogen in symbiosis is a common feature for Frankia cluster-2 strains, but which source is host-plant dependent. We also identified several gene losses.

The ammonium assimilation via the GS/GOGAT cycle for export to the host, entails a high demand of 2-oxoglutarate from the TCA cycle. This specialised metabolism seems to have led to genome reduction: we show that Frankia cluster-2 strains have lost the glyoxylate shunt and succinate semialdehyde dehydrogenase, leading to a linearization of the TCA cycle. This could explain the low saprotrophic potential of Frankia cluster-2.
The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass,Cenchrus ciliaris
Authors: Rathore Priyanka , Schwarzacher Trude , Heslop-Harrison J.S. (Pat) , Bhat Vishnu , Tomaszewska Paulina
Published: May 2022

Cenchrus ciliarisis an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found and we analysed here a 2n=4×+3=39 accession. The physical mapping of Ty1-copiaand Ty3-gypsyretroelements through fluorescencein situhybridization with global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. About a third of Ty1-copiasites overlapped or spanned centromeric DAPI positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methycytosine signals, except some Ty3-gypsyon the arms of chromosomes which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes ofC. ciliarisshowing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences ofC. ciliarisusing graph-based clustering. Probes developed from RepeatExplorer clusters gave strong signals mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploidC. ciliarislikely having different repeat sequence variants amplified before the genome came together in the tetraploid.
Low alcohol preferring mice have reduced task engagement during a waiting task for alcohol, which is enhanced by intermittent alcohol drinking
Authors: Starski Phillip , Maulucci Danielle , Mead Hunter , Hopf Frederic
Published: May 2022

Alcohol use disorder (AUD) is related to excessive binge alcohol consumption, and there is considerable interest in associated factors that promote intake. AUD has many behavioral facets that enhance inflexibility toward alcohol consumption, including impulsivity, motivation, and attention. Thus, it is important to understand how these factors might promote responding for alcohol and can change after protracted alcohol intake. Previous studies have explored such behavioral factors using responding for sugar in the 5-Choice Serial Reaction Time Task (5-CSRTT), which allows careful separation of impulsivity, attention, and motivation. Importantly, our studies uniquely focus on using alcohol as the reward throughout training and testing sessions, which is critical for beginning to answer central questions relating to behavioral engagement for alcohol. Alcohol preference and consumption in C57BL/6 mice were determined from the first 9 sessions of 2-hour alcohol drinking which were interspersed among 5-CSRTT training. Interestingly, alcohol preference but not consumption level significantly predicted 5-CSRTT responding for alcohol. In contrast, responding for strawberry milk was not related to alcohol preference. Moreover, high-preference (HP) mice made more correct alcohol-directed responses than low-preference (LP) during the first half of each session and had more longer reward latencies in the second half, with no differences when performing for strawberry milk, suggesting that HP motivation for alcohol may reflect “front-loading.” Mice were then exposed to an Intermittent Access to alcohol paradigm and retested in 5-CSRTT. While both HP and LP mice increased 5-CSRTT responding for alcohol, but not strawberry milk, LP performance rose to HP levels, with a greater change in correct and premature responding in LP versus HP. Overall, this study provides three significant findings: 1) alcohol was a suitable reward in the 5-CSRTT, allowing dissection of impulsivity, attention, and motivation in relation to alcohol drinking, 2) alcohol preference was a more sensitive indicator of mouse 5-CSRTT performance than consumption, and 3) chronic alcohol drinking promoted behavioral engagement with alcohol, especially for individuals with less initial engagement.
Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins
Authors: Zhang Fengwen , Zang Trinity , Stevenson Eva M. , Lei Xiao , Copertino Dennis C. , Mota Talia M. , Boucau Julie , Garcia-Beltran Wilfredo F. , Jones R. Brad , Bieniasz Paul D.
Published: May 2022

Viruses employ a variety of strategies to escape or counteract immune responses, including depletion of cell surface major histocompatibility complex class I (MHC-I), that would ordinarily present viral peptides to CD8+ cytotoxic T cells. As part of a screen to elucidate biological activities associated with individual SARS-CoV-2 viral proteins, we found that ORF7a reduced cell surface MHC-I levels by approximately 5-fold. Nevertheless, in cells infected with SARS-CoV-2, surface MHC-I levels were reduced even in the absence of ORF7a, suggesting additional mechanisms of MHC-I downregulation. ORF7a proteins from a sample of sarbecoviruses varied in their ability to induce MHC-I downregulation and, unlike SARS-CoV-2, the ORF7a protein from SARS-CoV lacked MHC-I downregulating activity. A single-amino acid at position 59 (T/F) that is variable among sarbecovirus ORF7a proteins governed the difference in MHC-I downregulating activity. SARS-CoV-2 ORF7a physically associated with the MHC-I heavy chain and inhibited the presentation of expressed antigen to CD8+ T-cells. Speficially, ORF7a prevented the assembly of the MHC-I peptide loading complex and causing retention of MHC-I in the endoplasmic reticulum. The differential ability of ORF7a proteins to function in this way might affect sarbecovirus dissemination and persistence in human populations, particularly those with infection- or vaccine-elicited immunity.