bluuebunny/crossref_metadata_2025 huggingface dataset:
Against Authority: The Bioethics of Ivermectin Use for COVID-19 Infection
Authors: Astărăstoae Vasile , Rogozea Liliana M.
Published: April 2023

Background:

The COVID-19 pandemic has brought new ethical challenges to both health care professionals and the general public. Among the ethical problems amplified during this period were the making of medical decisions to quickly introduce some drugs into therapeutic practice with unproven or insufficiently proven effects (such as ivermectin), the validity of drug testing, and the allocation of limited resources.

Fields of Uncertainty:

The COVID-19 pandemic brought to the attention of the entire scientific world a new problem, which exceeded the guidelines and rules known until then. Out of the desire to quickly solve this medical problem, a series of measures were taken, however not sufficiently validated in scientific terms; the recommendations regarding the use of drugs known for their properties to treat a greater number of conditions, such as ivermectin, was tried.

Data Sources:

A narrative review of the specialized literature was carried out using keywords such as COVID-19, ivermectin, ethics, and off-label medication from Scopus and Google Scholar but also of official documents developed at the international level (World Health Organization).

Ethics and Therapeutic Advances:

The off-label use of ivermectin alone or in combination with other medications during COVID pandemic raised problems related to the demonstration of its effectiveness, but also to ethics, starting from the expectations that both the medical staff and the population had of it. Ivermectin therapy was also evaluated by analyzing the behavior of ivermectin based on ethical principles (nonmaleficence, beneficence, and respect for one's autonomy) or on justice. Even in times of pandemic, exceptionalism must not triumph, and finding an effective treatment must be done through studies that respect ethical standard.

Conclusions:

The failures or rather lack of success in decision making during the pandemic showed that alongside scientific knowledge and the development of health policies, it is necessary to constantly evaluate the measures and decisions from an ethical point of view, and the prevention of slippages and abuses is not only necessary but even mandatory.
The effectiveness of unilateral isokinetic resistance training on cross-education is independent of contraction velocity: a case of female dorsiflexors and plantar flexors
Authors: Abazović Ensar , Kovačević Erol , Nakić Josipa , Peharec Stanislav , Paravlic Armin H.
Published: April 2023

The large body of published literature has shown that the effects of strength training can transfer from trained to untrained homologous limb muscles after unilateral training. These effects on strength have been shown to be very specific to the type and speed of training contraction. The aim of this study was to investigate the effects of a 4-week unilateral slow and fast velocity isokinetic concentric training, to compare the effects, and thus investigate whether these effects are speed-specific. Forty-four healthy female students allocated to slow training, fast training, or control performed 12 isokinetic concentric-concentric plantar/dorsal flexors training sessions (3 × 4 weeks) using their nondominant leg. Participants in the two experimental groups showed statistically significant gains in strength in both the trained (ranging from 8 to 41%) and untrained leg (5–26%), thus showing cross-education on strength effects. The present study demonstrated that 4 weeks (12 training sessions) of unilateral isokinetic resistance training in the concentric mode improved the strength of contralateral, untrained homologous muscles to the same extent, regardless of the contraction velocity used in females. Furthermore, the amount of concentric overload (50% more than during 60°/s) did not appear to affect the increase in strength gains. Therefore, practitioners are encouraged to use both training speeds when strength gains in the contralateral leg are the primary goal. If the training time is limited, however, training with a higher contraction speed is recommended.
Relative Pain Reduction and Duration of Nerve Block Response Predict Outcomes in Headache Surgery- A prospective cohort study
Authors: Knoedler Leonard , Chartier Christian , Casari Maria E. , Ortiz Ricardo , Odenthal Jan , Gfrerer Lisa , Austen William G.
Published: April 2023

Background:

Experts agree that nerve block (NB) response is an important tool in headache surgery screening. However, the predictive value of NBs remains to be proven in a prospective fashion.

Methods:

Pre- and post- NB visual analogue pain scores (0- 10) as well as duration of NB response were recorded prospectively. Surgical outcomes were recorded prospectively by calculating the Migraine Headache Index (MHI) preoperatively and postoperatively at 3 months, 12 months, and every year thereafter.

Results:

The study population included 115 patients. The chance of achieving MHI percent improvement of ≥80% was significantly higher in subjects who reported relative pain reduction of >60% following NB versus ≤60% (63/92, 68.5% versus 10/23, 43.5%; p= 0.03). Patients were more likely to improve their MHI ≥50% with relative pain reduction of >40% versus ≤40% (82/104, 78.8% versus 5/11, 45.5%; p= 0.01). In subjects with NB response of >15 days, 10 of 13 patients (77.0%) experienced MHI improvement of ≥80%. Notably, all of these patients (100%) reported MHI improvement of ≥50% with mean MHI improvement of 88%. Subjects with a NB response of ≥24 hours achieved significantly better outcomes than patients with a shorter response (72.7± 37.0% vs. 46.1± 39.7%; p= 0.02). However, of 14 patients reporting NB response of <24 hours, 4 patients had MHI improvement of ≥80% and 7 of ≥50%.

Conclusions:

Relative pain reduction and duration of NB response are predictors of MHI improvement after headache surgery. NBs are a valuable tool to identify patients who will benefit from surgery.
Remote fit wrist braces through artificial intelligence
Authors: Sedigh Ashkan , Townsend Clay , Khawam Sultan M. , Vaccaro Alexander R. , Carreras Britani N. , Beredjiklian Pedro K. , Rivlin Michael
Published: April 2023

Introduction:

Physical boundaries to access skilled orthotist or hand therapy care may be hindered by multiple factors, such as geography, or availability. This study evaluated the accuracy of fitting a prefabricated wrist splint using an app on a smart device. We hypothesize that remote brace fitting by artificial intelligence (AI) can accurately determine the brace size the patient needs without in-person fitting.

Methods:

Healthy volunteers were recruited to fit wrist braces. Using 2 standardized calibrated images captured by the smart device, each subject's image was loaded into the machine learning software (AI). Later, hand features were extracted, calibrated, and measured the application, calculated the correct splint size, and compared with the splint chosen by our subjects to improve its own accuracy. As a control (control 1), the subjects independently selected the best brace fit from an array of available splints. Subject selection was recorded and compared with the AI fit splint. As the second method of fitting (control 2), we compared the manufacturer recommended brace size (based on measured wrist circumference and provided sizing chart/insert brochure) with the AI fit splint.

Results:

A total of 54 volunteers were included. Thirty-two splints predicted by the algorithm matched the exact size chosen by each subject yielding 70% accuracy with a standard deviation of 10% (p < 0.001). The accuracy increased to 90% with 5% standard deviation if the splints were predicted within the next size category. Fit by manufacturer sizing chart was only 33% in agreement with participant selection.

Conclusion:

Remote brace fitting using AI prediction model may be an acceptable alternative to current standards because it can accurately predict wrist splint size. As more subjects were analyzed, the AI algorithm became more accurate predicting proper brace fit. In addition, AI fit braces are more than twice as accurate as relying on the manufacturer sizing chart.
Project Inspire pilot study: A hospital-led comprehensive intervention reduces gun violence among juveniles delinquent of gun crimes
Authors: Malone Kaleb , Hogue Antwan , Naman Edmond , Graves Curtis , Haiflich Andrew , Simmons Jon D. , Williams Ashley Y.
Published: April 2023

BACKGROUND

Gun violence disproportionately affects young Black men, but the impact extends to families and communities. Those at highest risk are teens delinquent of gun crimes. While there is no nationally accepted juvenile rate of recidivism, previous literature reveals rearrest rates from 50% to 80% in high-risk youth, and some reports show that up to 40% of delinquent juveniles are incarcerated in adult prisons before the age of 25 years. We hypothesize that Project Inspire, a hospital-led comprehensive intervention, reduces recidivism among high-risk teens.

METHODS

Led by a level 1 trauma center, key community stakeholders including the juvenile court, city, and city police department joined forces to create a community-wide program aimed at curbing gun violence in high-risk individuals. Participants, aged 13 to 18 years, are selected by the juvenile gun court. They underwent a rigorous 3-week program with a curriculum incorporating the following: trauma-informed training and confidence building, educational/professional development, financial literacy, entrepreneurship, and career-specific job shadowing and mentorship. Rates of recidivism were measured annually.

RESULTS

Project Inspire has hosted two classes in 2018 and 2019, graduating nine participants aged 14 to 17 years. Sixty-seven percent were Black. All were males. At 1 year, none of the graduates reoffended. At 2 years, one participant reoffended. At 3 years, no additional participants reoffended. No graduate reoffended as a juvenile. Thus, the overall rate of recidivism for Project Inspire is 11% to date. Eighty-nine percent of graduates received a diploma, general educational development, or obtained employment.

CONCLUSION

Project Inspire is a hospital-led initiative that effectively reduces recidivism among juveniles delinquent of gun crimes. This sets the framework for trauma centers nationwide to lead in establishing impactful, comprehensive, gun-violence intervention strategies.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level V.
T-DNA insertion mutagenesis in Penicillium brocae results in identification of an enolase gene mutant impaired in secretion of organic acids and phosphate solubilization
Authors: Zhang Juntao , Han Xiaoge , Su Yang , Staehelin Christian , Xu Changchao
Published: April 2023

Penicillium brocae strain P6 is a phosphate-solubilizing fungus isolated from farmland in Guangdong Province, China. To gain better insights into the phosphate solubilization mechanisms of strain P6, a T-DNA insertion population containing approximately 4500 transformants was generated by

Agrobacterium tumefaciens

-mediated transformation. The transformation procedure was optimized by using a Hybond N membrane for co-cultivation of

A. tumefaciens

and P. brocae. A mutant impaired in phosphate solubilization (named MT27) was obtained from the T-DNA insertion population. Thermal asymmetric interlaced PCR was then used to identify the nucleotide sequences flanking the T-DNA insertion site. The T-DNA in MT27 was inserted into the fourth exon of an enolase gene, which shows 90.8 % nucleotide identity with enolase mRNA from Aspergillus neoniger. Amino acid sequence homology analysis indicated that the enolase is well conserved among filamentous fungi and Saccharomyces cerevisiae. Complementation tests with the MT27 mutant confirmed that the enolase gene is involved in phosphate solubilization. Analysis of organic acids in culture supernatants indicated reduced levels of oxalic acid and lactic acid for the MT27 mutant compared to the parent strain P6 or the complementation strain. In conclusion, we suggest that the identified enolase gene of P. brocae is involved in production of specific organic acids, which, when secreted, act as phosphate solubilizing agents.
Neoadjuvant Chemotherapy plus Surgery versus Direct Surgery in Senile Patients with Gastric Cancer: Single-Center Retrospective Cohort Study
Authors: Sah Birendra Kumar , Yu Zhenjia , Li Jian , Lu Sheng , Zheng Yanan , Zhu Zhenglun , Li Chen , Yan Min , Zhu Zhenggang
Published: April 2023

Background

Despite the lack of decisive research advocating neoadjuvant chemotherapy there is a broad consensus that it is beneficial for gastric cancer in terms of survival. However, there is no comparative research on whether it is similarly helpful in senile patients with the age above 75 years old. Here we compared the survival rate between neoadjuvant plus surgery with Direct Surgery.

Methods

We analyzed 79 patients with locally advanced gastric cancer who were preoperatively suspicious of serosa positive or beyond (cT4a or cT4b); or extensive lymph node involvement (cN3). Postoperative complications and overall survival rate were compared between the patients who underwent neoadjuvant chemotherapy (NAC) plus surgery and the patients who had direct surgery.

Results

A total of 15 (19%) patients underwent neoadjuvant chemotherapy and 64 (81%) patients had direct surgery. The median follow-up time was 34 months (range of 24-60 months). While the median survival time was not reached in the direct surgery group, the median survival time for the NAC plus Surgery Group was 37 months. Two years of overall survival (OS) for the patients in the NAC plus Surgery group and direct surgery group were 53.3% and 70.3% respectively. There was no statistical difference between the two groups (p>0.05) in overall postoperative complication and length of postoperative stay.

Conclusions

Reduced does of neoadjuvant chemotherapy was feasible in senile patients. There was no difference in survival rate between the patients who had neoadjuvant plus surgery compared to those who had direct surgery. While this result contradicts the previous assumption that neoadjuvant chemotherapy is beneficial for late-stage gastric cancer patients, a well-controlled prospective study is mandatory for a better understanding of whether neoadjuvant chemotherapy is beneficial to senile patients too.
Social dialogue quality and workers’ health as perceived by Belgian trade union representatives during the COVID-19 pandemic
Authors: Wels Jacques , Hamarat Natasia , De Greef Vanessa
Published: April 2023

Background

Besides major employment disruptions, the COVID-19 pandemic has generated policy responses with specific mechanisms to protect workers’ health. In Belgium, most of these policies were negotiated at national and cross-sectorial level but implemented at company level with company-based collective negotiation playing a key role. This study examines the relationship between trade union representatives’ perception of social dialogue quality and change in workers’ physical and mental health in such a context.

Methods

Union representatives were surveyed throughout Belgium between August and December 2021 through an online questionnaire (N=469). We asked about the way they perceived workers’ physical and mental health within their companies and explain variations with the self-perceived change in quality of social dialogue as an exposure. We use a modified Poisson regression for binary outcomes on four stratified models that additively account for no control, company characteristics, pre-pandemic self-reported health and COVID-19-related measures. Weights are generated to ensure sector representativeness.

Results

30.1% of the sample reported a worsening social dialogue quality during the pandemic. Relative Risks (RR) of poor physical and mental health when social dialogue has worsened are respectively 1.49 [95%CI:1.03; 2.15] and 1.38 [95%CI= 1.09;1.74] when controlling for company characteristics and pre-pandemic health. Adding pandemic-related measures reduces the risk of both poor mental [RR=1.25; 95%CI: 0.84; 1.87] and physical health [RR=1.18; 95%CI:0.94;1.49].

Conclusions

Although based on self-reported variables, the study shows an association between poor social dialogue quality and poor physical and mental health during the COVID-19 pandemic that must be explored further in post-pandemic context.
Comparative analysis of anticholinergic burden scales to explain iatrogenic cognitive impairment and self-reported side effects in the euthymic phase of bipolar disorders: results from the FACE-BD cohort
Authors: Vidal N , Brunet-Gouet E , Frileux S , Aouizerate B , Aubin V , Belzeaux R , Courtet P , D’Amato T , Dubertret C , Etain B , Haffen E , Januel D , Leboyer M , Lefrere A , Llorca PM , Marlinge E , Olié E , Polosan M , Schwan R , Walter M ,   the FACE-BD (FondaMental Academic Centers of Expertise for Bipolar Disorders) group, Passerieux C , Roux P
Published: April 2023

Bipolar disorders (BD) are characterized by cognitive impairment during the euthymic phase, to which treatments can contribute. The anticholinergic properties of medications, i.e., the ability of a treatment to inhibit cholinergic receptors, are associated with cognitive impairment in elderly patients and people with schizophrenia but this association has not been well characterized in individuals with remitted bipolar disorders. Moreover, the validity of anticholinergic burden scales designed to assess the anticholinergic load of medications has been scarcely tested in bipolar disorders. We aimed to test the concurrent validity of several scales by assessing their associations with objective cognitive impairment and subjective anticholinergic side-effects in BD. We hypothesized that the scale is valid if its association with cognitive impairment or self-reported anticholinergic side-effects is significant. A sample of 2,031 individuals with euthymic bipolar disorders was evaluated with a neuropsychological battery to identify cognitive impairment. Two scales among 27 were significantly positively associated with cognitive impairment in multiple logistic regressions, whereas chlorpromazine equivalents, lorazepam equivalents, the number of antipsychotics, or the number of treatments were not. The two scales significantly correlated with worse performance in processing speed and verbal memory. In addition, 14 scales showed good concurrent validity to assess self-reported peripheral anticholinergic side-effects and 13 were valid for evaluating self-reported central anticholinergic side-effects. Thus, we identified valid scales to monitor the anticholinergic burden in BD, which may be useful in assessing iatrogenic cognitive impairment in studies investigating cognition in BD.
Generalized mutualisms promote range expansion in both plant and ant partners
Authors: Nathan Pooja , Economo Evan P. , Guénard Benoit , Simonsen Anna , Frederickson Megan E.
Published: April 2023

Mutualism improves organismal fitness, but strong dependence on another species can also limit a species’ ability to thrive in a new range if its partner is absent. We assembled a large, global dataset on mutualistic traits and species ranges to investigate how multiple plant-animal and plant-microbe mutualisms affect the spread of legumes and ants to novel ranges. We found that generalized mutualisms increase the likelihood that a species establishes and thrives beyond its native range, whereas specialized mutualisms either do not affect or reduce non-native spread. This pattern held in both legumes and ants, indicating that specificity between mutualistic partners is a key determinant of ecological success in a new habitat. Our global analysis shows that mutualism plays an important, if often overlooked, role in plant and insect invasions.
Sex-specific developmental changes in spinal cord pain pathways following neonatal inflammation
Authors: Hedley Kateleen E , Cuskelly Annalisa , Quinn Rikki K , Callister Robert J , Hodgson Deborah M , Tadros Melissa A
Published: April 2023

Early-life inflammation can have long lasting impact on pain processing and pain behaviours. For example, we have shown neonatal inflammation can result in changes within spinal neuronal networks and altered flinching of the hind paw following formalin injection three weeks later. This suggests mechanisms for altered pain behaviours lie in first and second order neurons in the pain neuroaxis. Exactly how these changes progress during postnatal development is not known. Accordingly, we investigated neuroinflammatory markers in sensory neurons (dorsal root ganglia; DRGs) and spinal cords of Wistar rats (both sexes) after early life inflammation. Rats were injected with LPS or saline on postnatal days (P) 3 and 5. DRGs and spinal cords (SC) were isolated on P7, 13 and 21, and the expression of six inflammatory mediators were quantified via RT-qPCR. In the DRG, four proinflammatory mediators were elevated in P7 rats exposed to LPS. By P13, only two proinflammatory agents were elevated, whereas at P21 the levels of all six inflammatory mediators were similar between LPS and saline-treated rats. There were no sex-specific differences in the expression profile of any mediator in DRGs. In the spinal cord this expression profile was reversed with no change in inflammatory mediators at P7, elevation of two at P13 and four at P21 in LPS treated rats. Interestingly, these differences were greater in the spinal cords of female rats, indicating sex-specific modulation of neuroinflammation even at these early stages of postnatal development. The increased inflammatory mediator profile in the spinal cords of P21 LPS-treated rats was accompanied by sex-specific modulation of astrocytic (GFAP) activation, with females showing an increase and males a decrease in GFAP following LPS exposure. Together, these data indicate sensory neurons are more susceptible to acute inflammation whereas inflammation in the spinal cord is delayed. The sex-specific modulation of inflammation during critical phases of development may help explain altered pain behaviours in adult males and females.
Ethnic inequalities among NHS staff in England - workplace experiences during the COVID-19 pandemic
Authors: Rhead Rebecca , Harber-Aschan Lisa , Onwumere Juliana , Polling Catherine , Dorrington Sarah , Ehsan Annahita , Stevelink Sharon AM , Khunti Kamlesh , Mir Ghazala , Morriss Richard , Wessely Simon , Woodhead Charlotte , Hatch Stephani L
Published: April 2023

Objectives

To determine how workplace experiences of NHS staff varied by ethnic group during the COVID-19 pandemic and examine how these experiences are associated with mental and physical health at the time of the study.

Methods

An online Inequalities Survey was conducted by the TIDES study (Tackling Inequalities and Discrimination Experiences in health Services) in collaboration with NHS CHECK. This Inequalities Survey collected measures relating to workplace experiences (such as personal protective equipment (PPE), risk assessments, redeployments, and discrimination) as well as mental health, and physical health from NHS staff working in the 18 trusts participating with the NHS CHECK study between February and October 2021 (N=4622).

Results

Regression analysis revealed that staff from Black and Mixed/Other ethnic groups had greater odds of experiencing workplace harassment (adjusted odds ratio (AOR) = 2.43 [1.56-3.78] and 2.38 [1.12-5.07], respectively) and discrimination (AOR = 4.36 [2.73-6.96], and 3.94 [1.67-9.33], respectively) compared to White British staff. Staff from black ethnic groups also had greater odds than White British staff of reporting PPE unavailability (AOR = 2.16 [1.16-4.00]). Such workplace experiences were associated with negative physical and mental health outcomes, though this association varied by ethnicity. Conversely, understanding employment rights around redeployment, being informed about, and having the ability to inform redeployment decisions were associated with lower odds of poor health outcomes.

Conclusions

Structural changes to the way staff from ethnically minoritised groups are supported, and how their complaints are addressed by leaders within the NHS are urgently required to address racism and inequalities in the NHS.

Policy implications

Maintaining transparency and implementing effective mechanisms for addressing poor working conditions, harassment, and discrimination is crucial in the NHS. This can be achieved through appointing a designated staff member, establishing a tracking system, and training HR managers in identifying and handling reports of racial discrimination. Incorporating diversity and inclusion considerations into professional development activities and providing staff with opportunities to actively participate in decision-making can also benefit their health. The NHS Workforce Race Equality Standard may need to broaden its scope to assess race equality effectively.
Total cerebral blood volume changes drive macroscopic cerebrospinal fluid flux in humans
Authors: Zimmermann Juliana , Boudriot Clara , Eipert Christiane , Hoffmann Gabriel , Nuttall Rachel , Neumaier Viktor , Bonhoeffer Moritz , Schneider Sebastian , Schmitzer Lena , Kufer Jan , Kaczmarz Stephan , Hedderich Dennis M , Ranft Andreas , Golkowski Daniel , Priller Josef , Zimmer Claus , Ilg Rüdiger , Schneider Gerhard , Preibisch Christine , Sorg Christian , Zott Benedikt
Published: April 2023

In the mammalian brain, the directed motion of cerebrospinal fluid (CSF-flux) is instrumental in the distribution and removal of solutes. Changes in total cerebral blood volume (CBV) have been hypothesized to drive CSF-flux. We tested this hypothesis in two multi-modal brain imaging experiments in healthy humans, in which we drove large changes in total CBV by neuronal burst-suppression under anesthesia, or by transient global vasodilation in a hypercapnic challenge. We developed a technique to monitor CBV changes based on associated changes in total brain volume by functional MRI (fMRI) and measured cerebral blood flow by arterial spin-labeling. Relating CBV-sensitive signals to fMRI-derived measures of macroscopic CSF flow across the basal cisternae, we demonstrate that increasing total CBV extrudes CSF from the skull and decreasing CBV allows its influx. Moreover, CSF largely stagnates when CBV is stable. Together, our results establish the direct coupling between total CBV changes and CSF-flux.
The influence of environment geometry on subiculum boundary vector cells in adulthood and early development
Authors: Muessig Laurenz , Rodrigues Fabio Ribeiro , Bjerknes Tale , Towse Ben , Barry Caswell , Burgess Neil , Moser Edvard I. , Moser May-Britt , Cacucci Francesca , Wills Thomas J.
Published: April 2023

Boundaries to movement form a specific class of landmark information used for navigation: Boundary Vector Cells (BVCs) are neurons which encode an animal’s location as a vector displacement from boundaries. Here we report the first objective characterisation of the prevalence and spatial tuning of subiculum BVCs. Manipulations of boundary geometry reveal two novel features of BVC firing. Firstly, BVC directional tunings align with environment walls in squares, but are uniformly distributed in circles, demonstrating that environmental geometry alters BVC receptive fields. Secondly, inserted barriers uncover both excitatory and inhibitory components to BVC receptive fields, demonstrating that inhibitory inputs contribute to BVC field formation. During post-natal development, subiculum BVCs mature slowly, contrasting with the earlier maturation of boundary-responsive cells in upstream Entorhinal Cortex. However, Subiculum and Entorhinal BVC receptive fields are altered by boundary geometry as early as tested, suggesting this is an inherent feature of the hippocampal representation of space.
Oleic acid decouples fecundity and longevity via DAF-12 steroid hormone signaling inC. elegans
Authors: Nichitean Alexandra M. , Compere Frances V. , Hall Sarah E.
Published: April 2023

In animals, early-life starvation can program gene expression changes that result in profound effects on adult phenotypes. ForC. elegansnematodes, passage through the stress-resistant dauer diapause stage due to early-life starvation establishes a cellular memory that manifests as increased metabolism and decreased fecundity compared to continuously developed adults. To further investigate the connection between metabolism and reproduction, we supplemented the diet of postdauer adults with different fatty acids and examined their life history traits. Here, we show that dietary oleic acid (OA) supplementation uniquely increases the fecundity of both postdauer and continuously developed adults in a DAF-12 steroid signaling dependent manner, potentially through the increased expression offat-7Δ9-desaturase andvit-2vitellogen genes. In addition, OA may rescue increased ferroptosis in postdauer germ lines and has complex effects on adult lifespan depending on the animals’ life history. Together, our results suggest a model where OA modifies DAF-12 activity to positively regulate fecundity, metabolism, and lifespan in adults.
Desmoplastic stroma restricts T cell extravasation and mediates immune exclusion and immunosuppression in solid tumors
Authors: Xiao Zebin , Todd Leslie , Huang Li , Noguera-Ortega Estela , Lu Zhen , Huang Lili , Kopp Meghan , Li Yue , Pattada Nimisha , Zhong Wenqun , Guo Wei , Scholler John , Liousia Maria , Assenmacher Charles-Antoine , June Carl H. , Albelda Steven M. , Puré Ellen
Published: April 2023

The desmoplastic stroma in solid tumors presents a formidable challenge to immunotherapies that rely on endogenous or adoptively transferred T cells, however, the mechanisms are poorly understood. To define mechanisms involved, we treat established desmoplastic pancreatic tumors with CAR T cells directed to fibroblast activation protein (FAP), an enzyme highly overexpressed on a subset of cancer-associated fibroblasts (CAFs). Depletion of FAP+CAFs results in loss of the structural integrity of desmoplastic matrix. This renders these highly treatment-resistant cancers susceptible to subsequent treatment with a tumor antigen (mesothelin)-targeted CAR and to anti-PD1 antibody therapy. Mechanisms include overcoming stroma-dependent restriction of T cell extravasation and/or perivascular invasion, reversing immune exclusion, relieving T cell suppression, and altering the immune landscape by reducing myeloid cell accumulation and increasing endogenous CD8+T cell and NK cell infiltration. These data provide strong rationale for combining tumor stroma-and malignant cell-targeted therapies to be tested in clinical trials.
Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators
Authors: Wait Sarah J. , Rappleye Michael , Lee Justin Daho , Smith Netta , Berndt Andre
Published: April 2023

Real-time monitoring of biological activity can be achieved through the use of genetically encoded fluorescent indicators (GEFIs). GEFIs are protein-based sensing tools whose biophysical characteristics can be engineered to meet experimental needs. However, GEFIs are inherently complex proteins with multiple dynamic states, rendering optimization one of the most challenging problems in protein engineering. Most GEFIs are engineered through trial-and-error mutagenesis, which is time and resource-intensive and often relies on empirical knowledge for each GEFI. We applied an alternative approach using machine learning to efficiently predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. We used the trained ensemble to perform an in silico functional screen on a library of 1423 novel, untested GCaMP variants. The mutations were predicted to significantly alter the fluorescent response, and off-rate kinetics were advanced for verification in vitro. We found that the ensemble’s predictions of novel variants’ biophysical characteristics closely replicated what we observed of the variants in vitro. As a result, we identified the novel ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, that achieve both faster kinetics and larger fluorescent responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, that outperforms the tested 6th, 7th, and 8th generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient prescreening of mutants for functional characteristics. By leveraging the learning capabilities of our ensemble, we were able to accelerate the identification of promising mutations and reduce the experimental burden associated with screening an entire library. Machine learning tools such as this have the potential to complement emerging high-throughput screening methodologies that generate massive datasets, which can be tedious to analyze manually. Overall, these findings have significant implications for developing new GEFIs and other protein-based tools, demonstrating the power of machine learning as an asset in protein engineering.
Assisting and Accelerating NMR Assignment with Restrained Structure Prediction
Authors: Liu Sirui , Chu Haotian , Xie Yuhao , Wu Fangming , Ni Ningxi , Wang Chenghao , Mu Fangjing , Wei Jiachen , Zhang Jun , Chen Mengyun , Li Junbin , Yu Fan , Fu Hui , Wang Shenlin , Tian Changlin , Wang Zidong , Gao Yi Qin
Published: April 2023

NMR experiments can detect in situ structures and dynamic interactions, but the NMR assignment process requires expertise and is time-consuming, thereby limiting its applicability. Deep learning algorithms have been employed to aid in experimental data analysis. In this work, we developed a RASP model which can enhance structure prediction with restraints. Based on the Evoformer and structure module architecture of AlphaFold, this model can predict structure based on sequence and a flexible number of input restraints. Moreover, it can evaluate the consistency between the predicted structure and the imposed restraints. Based on this model, we constructed an iterative NMR NOESY peak assignment pipeline named FAAST, to accelerate assignment process of NOESY restraints and obtaining high quality structure ensemble. The RASP model and FAAST pipeline not only allow for the leveraging of experimental restraints to improve model prediction, but can also facilitate and expedite experimental data analysis with their integrated capabilities.
Viral pIC-pocketing: RSV sequestration of eIF4F Initiation Complexes into bi-phasic biomolecular condensates
Authors: Jobe Fatoumatta , Kelly James T. , Simpson Jennifer , Wells Joanna , Armstrong Stuart D , Spick Matt , Lacey Emily , Logan Leanne , Geifman Nophar , Hawes Philippa , Bailey Dalan
Published: April 2023

Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Herein, we report a strategy whereby the orthopneumoviruses sequester various components of the eiF4FInitiationComplex machinery into viral IBs to facilitate translation of their own mRNAs; pIC-pocketing. Mass spectrometry analysis of sub-cellular fractions from RSV-infected cells identified significant modification of the cellular translation machinery; however; interestingly, ribopuromycylation assays showed no changes to global levels of translation. Electron micrographs of RSV-infected cells revealed bi-phasic organisation of IBs; specifically, spherical “droplets” nested within the larger inclusion. Using correlative light and electron microscopy (CLEM), combined with fluorescence in situ hybridisation (FISH), we showed that the observed bi-phasic morphology represents functional compartmentalisation of the IB and that these domains are synonymous with the previously reported inclusion body associated granules (IBAGs). Detailed analysis demonstrated that IBAGs concentrate nascent viral mRNA, the viral M2-1 protein as well as many components of the eIF4F complex, involved in translation initiation. Interestingly, although ribopuromycylation-based imaging indicates the majority of viral mRNA translation likely occurs in the cytoplasm, there was some evidence for intra-IBAG translation, consistent with the likely presence of ribosomes in a subset of IBAGs imaged by electron microscopy. The mechanistic basis for this pathway was subsequently determined; the viral M2-1 protein interacting with eukaryotic translation initiation factor 4G (eIF4G) to facilitate its transport between the cytoplasm and the separate phases of the viral IB. In summary, our data shows that IBs function to spatially regulate early steps in viral translation within a highly selective biphasic liquid organelle.
Chromatin structure and context-dependent sequence features control prime editing efficiency
Authors: Kim Somang , Yuan Jimmy B. , Woods Wendy S. , Newton Destry A. , Perez-Pinera Pablo , Song Jun S.
Published: April 2023

Prime editor (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer binding site (PBS) and reverse transcription (RT) template regions of PE guide-RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5’ to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and seen to depend on both PBS and RT template lengths. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.
Molecular, metabolic and functional CD4 T cell paralysis impedes tumor control
Authors: Guo Mengdi , Abd-Rabbo Diala , Bertol Bruna , Carew Madeleine , Lukhele Sabelo , Snell Laura M , Xu Wenxi , Boukhaled Giselle M , Elsaesser Heidi , Halaby Marie jo , Hirano Naoto , McGaha Tracy L , Brooks David G
Published: April 2023

CD4 T cells are important effectors of anti-tumor immunity, yet the regulation of CD4 tumor-specific T (TTS) cells during cancer development is still unclear. We demonstrate that CD4 TTScells are initially primed in the tumor draining lymph node and begin to divide following tumor initiation. Distinct from CD8 TTScells and previously defined exhaustion programs, CD4 TTScell proliferation is rapidly frozen in place and differentiation stunted by a functional interplay of T regulatory cells and both intrinsic and extrinsic CTLA4 signaling. Together these mechanisms paralyze CD4 TTScell differentiation, redirecting metabolic and cytokine production circuits, and reducing CD4 TTScell accumulation in the tumor. Paralysis is actively maintained throughout cancer progression and CD4 TTScells rapidly resume proliferation and functional differentiation when both suppressive reactions are alleviated. Strikingly, Treg depletion alone reciprocally induced CD4 TTScells to themselves become tumor-specific Tregs, whereas CTLA4 blockade alone failed to promote T helper differentiation. Overcoming their paralysis established long-term tumor control, demonstrating a novel immune evasion mechanism that specifically cripples CD4 TTScells to favor tumor progression.
Cytomixis and aberrant phenomena during meiosis in pollen mother cells ofCamellia sinensisvar.sinensiscv ‘Fudingdabai’
Authors: Yu Xuelian , You Xinhan , Zhang Lixia , Li Xingfeng
Published: April 2023

Tea plant (Camellia sinensis) is an economically essential crop in China, Japan and other countries. The present study reports the meiotic behavior, including microsporogenesis of the ‘Fudingdabai’ cultivar inCamellia sinensisvar.sinensis. Most of the investigated pollen mother cells undergo normal meiosis processes. In contrast, a few of the pollen mother cells showed some abnormal phenomena such as cytomixis, monovalent, laggard chromosomes, unsynchronized division, micronucleus, and so on. Among which, spontaneous cytomixis is the most common phenomenon, which mainly occurred in early prophase I but also in meiosis II. Other abnormal phenomena were less than cytomixis. The results of this study laid a foundation for exploring the meiosis and cytogenetics study of the tea plants.
A workcell 1.0 for programmable and controlled operation of multiple fluidic chips in parallel
Authors: Ning Chuanfang , Bunke Gabriel , Lietar Simon , van den Heuvel Lukas , Shahein Amir
Published: April 2023

We developed a versatile lab-on-chip (LOC) workcell that enables the design and automatic execution of experiments on LOC devices, improving how we establish, optimize, and productionalize LOC processes. Key features include direct docking and cooling of native laboratory tubes, programmable reagent mixing and dilutions, parallel operation of multiple chips, precise flowrate and pressure control, clogging detection and response, programmable microscope control, chip temperature regulation, and scheduled cleaning. All functionality is controlled seamlessly from an easy-to-write protocol file, and based on extensible hardware and software infrastructures to promote community development. To showcase the platform’s use and versatility, we demonstrate a series of 5 different automated experiments at varying levels of complexity, executed across both Quake-valve and droplet microfluidic systems. In particular, the workcell was instructed to map the parameter regime that generates viable droplets, to allow a user to select diameters and production frequencies of interest for single bacterial cell encapsulation. Furthermore, three out of three days in a row, the platform successfully performed a complex 15.5h long experiment, integrating in a single automated protocol the full core workflow required by a typical protein-characterization lab: protein expression, purification, dilution generation, and quantitative binding characterization (generating 55296 images in the process). Experiments conducted through the workcell are easier to set up, offer increased control over experiment conditions and parameters, and can be heavily parallelized.
FAO-supported OxPhos leukemic stem cells are sensitive to cold
Authors: Griessinger Emmanuel , Pereira-Martins Diego , Nebout Marielle , Bosc Claudie , Saland Estelle , Boet Emilie , Sahal Ambrine , Chiche Johanna , Debayle Delphine , Fleuriot Lucille , Pruis Maurien , De Mas Véronique , Vergez François , Récher Christian , Huls Gerwin , Sarry Jean-Emmanuel , Schuringa Jan Jacob , Peyron Jean-François
Published: April 2023

Targeting mitochondrial oxidative phosphorylation (OxPhos) metabolism has revealed a potential weakness for leukemic stem cells (LSCs) that can be exploited for therapeutic purposes. Fatty acids oxidation (FAO) is a crucial OxPhos-fueling catabolic pathway for some AML and for chemotherapy-resistant AML cells. Here, we identified cold sensitivity at 4°C (cold killing challenge: CKC4), as a novel vulnerability that selectively kills FAO-supported OxPhos LSCs in Acute Myeloid Leukemia while sparing normal hematopoietic stem cells (HSCs). Cell death of OxPhos leukemic cells was induced by membrane permeabilization at 4°C while by sharp contrast, leukemic cells relying on glycolysis were resistant. Forcing glycolytic cells into OxPhos metabolism sensitized them to CKC4. We show using lipidomic and proteomic analyzes that OxPhos shapes the composition of the plasma membrane and introduce variation of 22 lipid subfamilies between cold-sensitive and cold-resistant cells. Cold sensitivity is a potential OxPhos biomarker.

Significance

This study reveals that mitochondrial energetics fueled by FAO metabolism introduces membrane fragility upon cold exposure in OxPhos-driven AMLs and in LSCs. This novel physical property of Leukemic cells and LSCs opens new avenues for biomarker and diagnostics as well as for anti-OxPhos drug screening and LSCs targeting.

One Sentence Summary

OxPhos leukemic cells die at 4°C
Automatic measurement of cardiothoracic ratio in chest x-ray images with ProGAN-generated dataset
Authors: Kusakunniran Worapan , Saiviroonporn Pairash , Siriapisith Thanongchai , Tongdee Trongtum , Uraiverotchanakorn Amphai , Leesakul Suphawan , Thongnarintr Penpitcha , Kuama Apichaya , Yodprom Pakorn
Published: April 2023

Purpose

The cardiomegaly can be determined by the cardiothoracic ratio (CTR) which can be measured in a chest x-ray image. It is calculated based on a relationship between a size of heart and a transverse dimension of chest. The cardiomegaly is identified when the ratio is larger than a cut-off threshold. This paper aims to propose a solution to calculate the ratio for classifying the cardiomegaly in chest x-ray images.

Design/methodology/approach

The proposed method begins with constructing lung and heart segmentation models based on U-Net architecture using the publicly available datasets with the groundtruth of heart and lung masks. The ratio is then calculated using the sizes of segmented lung and heart areas. In addition, Progressive Growing of GANs (PGAN) is adopted here for constructing the new dataset containing chest x-ray images of three classes including male normal, female normal and cardiomegaly classes. This dataset is then used for evaluating the proposed solution. Also, the proposed solution is used to evaluate the quality of chest x-ray images generated from PGAN.

Findings

In the experiments, the trained models are applied to segment regions of heart and lung in chest x-ray images on the self-collected dataset. The calculated CTR values are compared with the values that are manually measured by human experts. The average error is 3.08%. Then, the models are also applied to segment regions of heart and lung for the CTR calculation, on the dataset computed by PGAN. Then, the cardiomegaly is determined using various attempts of different cut-off threshold values. With the standard cut-off at 0.50, the proposed method achieves 94.61% accuracy, 88.31% sensitivity and 94.20% specificity.

Originality/value

The proposed solution is demonstrated to be robust across unseen datasets for the segmentation, CTR calculation and cardiomegaly classification, including the dataset generated from PGAN. The cut-off value can be adjusted to be lower than 0.50 for increasing the sensitivity. For example, the sensitivity of 97.04% can be achieved at the cut-off of 0.45. However, the specificity is decreased from 94.20% to 79.78%.