bluuebunny/crossref_metadata_2025 huggingface dataset:
Ice plant root plasma membrane aquaporins are regulated by clathrin-coated vesicles in response to salt stress
Authors: Gómez-Méndez María Fernanda , Amezcua-Romero Julio César , Rosas-Santiago Paul , Hernández-Domínguez Eric Edmundo , de Luna-Valdez Luis Alberto , Ruiz-Salas Jorge Luis , Vera-Estrella Rosario , Pantoja Omar
Published: November 2022

The regulation of root Plasma membrane (PM) Intrinsic Protein (PIP)-type aquaporins (AQPs) is potentially important for salinity tolerance. However, the molecular and cellular details underlying this process in halophytes remain unclear. Using free-flow electrophoresis and label-free proteomics, we report that the increased abundance of PIPs at the PM of the halophyte ice plant (Mesembryanthemum crystallinum L.) roots under salinity conditions is regulated by clathrin-coated vesicles (CCV). To understand this regulation, we analyzed several components of the M. crystallinum CCV complexes: clathrin light chain (McCLC) and subunits μ1 and μ2 of the adaptor protein (AP) complex (McAP1μ and McAP2μ). Co-localization analyses revealed the association between McPIP1;4 and McAP2μ and between McPIP2;1 and McAP1μ, observations corroborated by mbSUS assays, suggesting that AQP abundance at the PM is under the control of CCV. The ability of McPIP1;4 and McPIP2;1 to form homo- and hetero-oligomers was tested and confirmed, as well as their activity as water channels. Also, we found increased phosphorylation of McPIP2;1 only at the PM in response to salt stress. Our results indicate root PIPs from halophytes might be regulated through CCV trafficking and phosphorylation, impacting their localization, transport activity, and abundance under salinity conditions.
Methotrexate, leflunomide and tacrolimus use and the progression of rheumatoid arthritis-associated interstitial lung disease
Authors: Kim Ji-Won , Chung Sang Wan , Pyo Jung Yoon , Chang Sung Hae , Kim Min Uk , Park Chan Ho , Lee Ji Sung , Lee Jeong Seok , Ha You-Jung , Kang Eun Ha , Lee Yeon-Ah , Park Yong-Beom , Lee Eun Young , Choe Jung-Yoon
Published: November 2022

Objective

To examine the association between MTX, LEF and tacrolimus use and the progression of RA-associated interstitial lung disease (ILD).

Methods

The Korean RA-ILD cohort prospectively enrolled patients with RA-associated ILD at multiple centres from 2015 to 2018 and followed up with them for 3 years. ILD progression was defined by any of the followings: a decrease of ≥10% in forced vital capacity, a decrease of ≥15% in the diffusing capacity of the lung for carbon monoxide, or death from respiratory failure.

Results

Of 143 patients, 64 patients experienced ILD progression during a median follow-up period of 33 months. The use of MTX [adjusted hazard ratio (aHR), 1.06; 95% CI, 0.59, 1.89], LEF (aHR, 1.75; 95% CI, 0.88, 3.46) and tacrolimus (aHR, 0.94; 95% CI, 0.52, 1.72) did not increase the risk of ILD progression. However, the association between LEF use and the risk of ILD progression was significant in subgroups with poor lung function (aHR, 8.42; 95% CI, 2.61, 27.15). Older age, male sex, a shorter RA duration, higher RA disease activity and extensive disease at baseline were independently associated with ILD progression.

Conclusion

None of the three treatments increased the risk of RA-associated ILD progression, except for LEF, which increased the risk of ILD progression in patients with severe ILD. The appropriate use of conventional synthetic disease-modifying antirheumatic drugs considering RA disease activity and ILD severity would be important for the management of RA-associated ILD.
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process
Authors: Barido-Sottani Joëlle , Żyła Dagmara , Heath Tracy A
Published: November 2022

Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.]
Predictive encoding of pure tones and FM-sweeps in the human auditory cortex
Authors: Stein Jasmin , von Kriegstein Katharina , Tabas Alejandro
Published: November 2022

Expectations substantially influence perception, but the neural mechanisms underlying this influence are not fully understood. A prominent view is that sensory neurons encode prediction error with respect to expectations on upcoming sensory input. Although the encoding of prediction error has been previously demonstrated in the human auditory cortex (AC), previous studies often induced expectations using stimulus repetition, potentially confounding prediction error with neural habituation. These studies also measured AC as a single population, failing to consider possible predictive specializations of different AC fields. Moreover, the few studies that considered prediction error to stimuli other than pure tones yielded conflicting results. Here, we used functional magnetic resonance imaging (fMRI) to systematically investigate prediction error to subjective expectations in auditory cortical fields Te1.0, Te1.1, Te1.2, and Te3, and two types of stimuli: pure tones and frequency modulated (FM) sweeps. Our results show that prediction error is elicited with respect to the participants’ expectations independently of stimulus repetition and similarly expressed across auditory fields. Moreover, despite the radically different strategies underlying the decoding of pure tones and FM-sweeps, both stimulus modalities were encoded as prediction error in most fields of AC. Altogether, our results provide unequivocal evidence that predictive coding is the general encoding mechanism in AC.
Voices of Women With Lived Experience of Substance Use During Pregnancy
Authors: Hilliard Florence , Goldstein Ellen , Nervik Kendra , Croes Kenneth , Ossorio Pilar N. , Zgierska Aleksandra E.
Published: November 2022

Despite concerns about negative neurocognitive effects of in utero substance exposure on child and brain development, research in this area is limited. This study gathered perspectives of persons with lived experience of substance use (eg, alcohol, prescription and illicit opioids, and other illicit substances) during a previous pregnancy to determine facilitators and barriers to research engagement in this vulnerable population. We conducted structured, in-depth, individual interviews and 2 focus groups of adult persons with lived experience of substance use during a previous pregnancy. Questions were developed by clinical, research, bioethics, and legal experts, with input from diverse stakeholders. They inquired about facilitators and barriers to research recruitment and retention, especially in long-term studies, with attention to bio-sample and neuroimaging data collection and legal issues. Interviews and focus groups were audio-recorded, transcribed, and analyzed using inductive coding qualitative analysis methods. Ten participants completed in-depth interviews and 7 participated in focus groups. Three main themes emerged as potential barriers to research engagement: shame of using drugs while pregnant, fear of punitive action, and mistrust of health care and research professionals. Facilitative factors included trustworthiness, compassion, and a nonjudgmental attitude among research personnel. Inclusion of gender-concordant recovery peer support specialists as research team members was the most frequently identified facilitator important for helping participants reduce fears and bolster trust in research personnel. In this qualitative study, persons with lived experience of substance use during a previous pregnancy identified factors critical for engaging this population in research, emphasizing the involvement of peer support specialists as research team members.
Statewide Physician Survey Regarding Pediatric Muslim Fasting
Authors: Dabaja Emman , Haidous Muhammad , Shihan Hadeel , Haidar-El-Atrache Sara
Published: November 2022

During Ramadan, Muslims fast from dawn to dusk for the duration of the month. The current literature focuses on adults who fast, with little attention to pediatric practices. An anonymous, digital survey was conducted using Qualtrics software and distributed to residents, fellows, or attendings in Michigan in 2019. Overall, 278 participants were included in the analysis, with 87% (242/278) identifying as pediatric trained physicians. In all, 82% (228/278) of physicians identified as non-Muslim and 76% (211/278) had never partaken in the Muslim fast. About 52% (141/273) of participants had at least a moderate amount of exposure to Muslim pediatric patients in their clinical practice. Most physicians (66%; 175/265) reported they never asked their pediatric patients or their families about fasting. About 61% (167/273) of participants rated their understanding of fasting as minimal to none. Another 52% (142/273) of participants reported feeling somewhat or extremely uncomfortable discussing fasting recommendations with their pediatric patients and their families. Our study is the first of its kind in assessing current knowledge and practice regarding pediatric Muslim fasting among physicians in the United States. In addition, it highlights a gap in physicians' understanding and comfort in providing anticipatory guidance for their Muslim patients.
Women’s Lived Experience of the Interconnectedness of Trauma, Substance Use, and Prison
Authors: Vilhjalmsdottir Arndis , Halldorsdottir Sigridur , Sigurdardottir Sigrún
Published: November 2022

The aim of the study was to explore women's experience of Icelandic prisons and of the interconnectedness of trauma, substance use, and prison. Nine incarcerated women, 20–45 years old, participated in this phenomenological study. One or two in-depth interviews were conducted with each participant, in all 16 interviews. The interconnectedness of trauma, substance use, and prison was evident in the participants' accounts. The participants had experienced severe traumas, in childhood and/or in adult life, most of it caused by recurrent experience of violence, bullying, neglect, and beatings and later violent relationships. For the participants, substance use was an unhelpful coping strategy intended to numb severe emotional distress. Most of the participants used substances intravenously that had progressed incredibly fast from initial drug use. They had tried most of the addiction treatments available to them, none of which were trauma based. Participants struggled with complex physical and mental health problems related to substance use and previous traumas but often felt prejudged when they sought healthcare services. They experienced being in prison as depersonalizing and dehumanizing. Most of them were mothers and had lost custody of their children because of substance use causing some of them deep grief. Participants called for more active substance treatment programs in prisons and complained about idleness that they felt increased their addiction. As a conclusion, we call for a trauma-informed care approach in prisons for women to prevent revictimization as well as to assist with mental health issues and substance use.
The Scientific Rigor of the Objective Structured Examination for Competency Assessment in Health Sciences Education: A Systematic Review
Authors: Pelland Lucie , Kolomitro Klodiana , Hopkins-Rosseel Diana , Durando Paola
Published: November 2022

Background and Purpose.

The objective structured clinical examination (OSCE) is widely used as an assessment of competency in health sciences education. The aim of our systematic review was to appraise the scientific rigor of the OSCE as a competency-based assessment in health sciences education, including physical therapy.

Methods.

Our search was performed in 6 databases—Ovid MEDLINE(R), CINAHL, EMBASE, APA PsycINFO, ERIC, and Web of Science—to identify original data evaluating the OSCE in programs of education in physical therapy and related health sciences disciplines. Data were extracted as per the Utility Model to evaluate the validity, educational impact, reliability, acceptability, and costs of the OSCE in these programs.

Results.

The search identified 106 records, with 13 studies meeting our eligibility criteria. The OSCE is distinct from traditional clinical assessments, with low-to-fair concurrent validity between the 2 assessment types. The OSCE was used for instructional design, namely, curriculum development and alignment, and for educational practice, namely, making decisions on students' readiness for practice. Limitations of the OSCE include poor-to-low validity to predict practice readiness and low-to-acceptable reliability, with student-specific, domain-specific, and examiner-specific effects on outcomes identified. Strategies were provided which could improve the scientific rigor of the OSCE.

Discussion and Conclusion.

Based on current evidence, the scientific rigor of the OSCE may be insufficient to support its use to make academic decisions on students' standing in health sciences programs, including physical therapy, and readiness for clinical practice, with confidence. However, the OSCE can play an important role in instructional design and in guiding student learning.

Protocol registration:

PROSPERO, ID 162338.
TRAINED IMMUNITY: A POTENTIAL APPROACH FOR IMPROVING HOST IMMUNITY IN NEONATAL SEPSIS
Authors: Polcz Valerie E. , Rincon Jaimar C. , Hawkins Russell B. , Barrios Evan L. , Efron Philip A. , Moldawer Lyle L. , Larson Shawn D.
Published: November 2022

Sepsis, a dysregulated host immune response to infection, is one of the leading causes of neonatal mortality worldwide. Improved understanding of the perinatal immune system is critical to improve therapies to both term and preterm neonates at increased risk of sepsis. Our narrative outlines the known and unknown aspects of the human immune system through both the immune tolerant in utero period and the rapidly changing antigen-rich period after birth. We will highlight the key differences in innate and adaptive immunity noted through these developmental stages and how the unique immune phenotype in early life contributes to the elevated risk of overwhelming infection and dysregulated immune responses to infection upon exposure to external antigens shortly after birth. Given an initial dependence on neonatal innate immune host responses, we will discuss the concept of innate immune memory, or “trained immunity,” and describe several potential immune modulators, which show promise in altering the dysregulated immune response in newborns and improving resilience to sepsis.
Viscous froth model applied to the dynamic simulation of bubbles flowing in a channel: three-bubble case
Authors: Torres-Ulloa C. , Grassia P.
Published: November 2022

A two-dimensional foam system comprised of three bubbles is studied via simulations with the viscous froth model. Bubbles are arranged in a so-called staircase configuration and move along a channel due to imposed driving back pressure. This flowing three-bubble system has been studied previously on the basis that it interpolates between a simpler staircase structure (a simple lens, which breaks up via so-called topological transformations if driven at high pressure) and an infinite staircase (which sustains arbitrarily large driving pressure without breaking). Depending on bubble size relative to channel size, different solution branches for the three-bubble system were found: certain branches terminate (as for the simple lens) in topological transformations and others reach (as for an infinite staircase) a geometrically invariant migrating state. The methodology used previously was, however, a purely steady state one, and hence did not interrogate stability of the various branches, nor the role of imposing different driving pressures upon topological transformation type. To address this, unsteady state three-bubble simulations are realized here. Stable solution branches without topological transformation exist for comparatively low driving pressures. For sufficiently high imposed back pressures, however, topological transformations occur, albeit with imposed pressure now influencing the transformation type.
A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I
Authors: Kayigwe Ahab N. , M. Darby Jocelyn , Lyons A. Bruce , L. Patchett Amanda , Lisowski Leszek , Liu Guei-Sheung , S. Flies Andrew
Published: November 2022

The devil facial tumour disease (DFTD) has led to a massive decline in the wild Tasmanian devil (Sarcophilus harrisii) population. The disease is caused by two independent devil facial tumours (DFT1 and DFT2). These transmissible cancers have a mortality rate of nearly 100 %. An adenoviral vector-based vaccine has been proposed as a conservation strategy for the Tasmanian devil. This study aimed to determine if a human adenovirus serotype 5 could express functional transgenes in devil cells. As DFT1 cells do not constitutively express major histocompatibility complex class I (MHC-I), we developed a replication-deficient adenoviral vector that encodes devil interferon gamma (IFN-γ) fused to a fluorescent protein reporter. Our results show that adenoviral-expressed IFN-γ was able to stimulate upregulation of beta-2 microglobulin, a component of MHC-I, on DFT1, DFT2 and devil fibroblast cell lines. This work suggests that human adenoviruses can serve as a vaccine platform for devils and potentially other marsupials.
Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review
Authors: Fernández-Alonso Melissa , Aguirre Camorlinga Andrea , Messiah Sarah E. , Marroquin Elisa
Published: November 2022

Introduction. Millions of antibiotic prescriptions are written annually in the USA.

Gap Statement. Probiotics reduce antibiotic-induced gastrointestinal side effects; however, the effect of probiotics on preserving gut microbial composition in response to antibiotics is not well understood.

Aim. To evaluate whether the addition of probiotics is capable of reverting the changes in alpha diversity and gut microbial composition commonly observed in adult participants receiving antibiotics.

Methodology. A search was conducted by two researchers following the PRISMA guidelines using PubMed, Science Direct, Cochrane and Embase from January to December 2021 with the following inclusion criteria: (i) randomized clinical trials assessing the effect of antibiotics, probiotics or antibiotics+probiotics; (ii) 16S rRNA; (iii) adult participants; and (iv) in English. Once data was extracted in tables, a third researcher compared, evaluated and merged the collected data. The National Institutes of Health (NIH) rating system was utilized to analyse risk of bias.

Results. A total of 29 articles (n=11 antibiotics, n=11 probiotics and n=7 antibiotics+probiotics) met the inclusion criteria. The lack of standardization of protocols to analyse the gut microbial composition and the wide range of selected antibiotics/probiotics complicated data interpretation; however, despite these discrepancies, probiotic co-administration with antibiotics seemed to prevent some, but not all, of the gut microbial diversity and composition changes induced by antibiotics, including restoration of health-related bacteria such as

Faecalibacterium prausnitzii

.

Conclusion. Addition of probiotics to antibiotic interventions seems to preserve alpha diversity and ameliorate the changes to gut microbial composition caused by antibiotic interventions.
Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized inUstilago maydis
Authors: Philipp Magnus , Müller Lisa , Andrée Marcel , Hussnaetter Kai P. , Schaal Heiner , Feldbrügge Michael , Schipper Kerstin
Published: November 2022

The COVID-19 pandemic has greatly impacted the global economy and health care systems, illustrating the urgent need for timely and inexpensive responses to a pandemic threat in the form of vaccines and antigen tests. The causative agent of COVID-19 is SARS-CoV-2. The spike protein on the virus surface interacts with the human angiotensin-converting enzyme (ACE2) via the so-called receptor binding domain (RBD), facilitating virus entry. The RBD thus represents a prime target for vaccines, therapeutic antibodies, and antigen test systems. Currently, antigen testing is mostly conducted by qualitative flow chromatography or via quantitative ELISA-type assays. The latter mostly utilize materials like protein-adhesive polymers and gold or latex particles. Here we present an alternative ELISA approach using inexpensive materials and permitting quick detection based on components produced in the microbial modelUstilago maydis. In this fungus, heterologous proteins like biopharmaceuticals can be exported by fusion to unconventionally secreted chitinase Cts1. As a unique feature, the carrier chitinase binds to chitin allowing its additional use as a purification or immobilization tag. In this study, we produced different mono- and bivalent SARS-CoV-2 nanobodies directed against the viral RBD as Cts1 fusions and screened their RBD binding affinityin vitroandin vivo. Functional nanobody-Cts1 fusions were immobilized on chitin forming an RBD tethering surface. This provides a solid base for future development of an inexpensive antigen test utilizing unconventionally secreted nanobodies as RBD trap and a matching ubiquitous and biogenic surface for immobilization.
Epidemiology of Extended-spectrum beta-lactamase-producingEscherichia coliat the human-animal-environment interface in Wakiso district, Uganda
Authors: Muleme James , Musoke David , Balugaba Bonny E. , Kisaka Stevens , Makumbi Frederick E. , Buregyeya Esther , Isunju John B. , Rogers Wambi , Mugambe Richard K. , Kankya Clovice , Munyeme Musso , Ssempebwa John C.
Published: November 2022

Background

Extended-spectrum beta-lactamase-producingEscherichia coli(ESBL-PE) represents a significant global public health concern. Much as humans, animals and environments harbor ESBL-PE, its epidemiology in Uganda is still not well understood. This study explains the epidemiology of ESBL-PE using the one health approach in selected farming households in Wakiso district, central Uganda.

Methodology

Environmental, human, and animal samples were collected from 104 households. Additional data were obtained using observation checklists and through interviews with household members using a semi-structured questionnaire. Surface swabs, soil, water, human and animal fecal samples were introduced onto ESBL chromogenic agar. The isolates were identified using biochemical tests and double-disk synergy tests. To assess associations, prevalence ratios (PRs) were computed using a generalized linear model (GLM) analysis with modified Poisson and a log link with robust standard errors in R software.

Results

A total of 82.7% (86/104) households had at least one positive ESBL-PE isolate. The overall prevalence of ESBL-PE at the human-animal-environment interface was approximately 25.0% (95% CI: 22.7-28.3). Specifically, animals, environment and humans had an ESBL-PE prevalence of 35.4%, 5.8%, and 45.4% respectively. Having visitors (adj PR= 1.19, 95% CI: 1.04-1.36), utilizing veterinary services (adj PR= 1.39, 95% CI: 1.20-1.61) and using animal waste for gardening (adj PR= 1.29, 95% CI: 1.05-1.60) were positively associated with ESBL-PE contamination. However, covering the drinking water container with a lid (adj PR= 0.84 95% CI: 0.73-0.96) was associated with absence of ESBL-PE.

Conclusion

There is wider dissemination of ESBL-PE in the environment, humans, and animals, indicating poor infection prevention and control (IPC) measures in the area. Improved collaborative one health mitigation strategies such as safe water chain, farm biosecurity, household and facility-based IPC measures are recommended to reduce the burden of antimicrobial resistance at community level.
Analysis of IGHA1 and other salivary proteins post half marathon in female participants
Authors: Maruyama Yosuke , Seki Tomoaki , Ando Seiichi , Tanabe Hiroki , Mori Hitoshi
Published: November 2022

Background

High intensity exercise, such as in marathons and triathlons, suppresses transient local and systemic immunity. Much is known about the systemic immunosuppression response, but little is known about its local response in the oral cavity, lungs, bronchial tubes, and skin. The oral cavity is an entrance for bacteria or viruses to enter the body. Saliva covers the epidermis of the oral cavity and plays an important role in the local stress response by preventing infection. In this study, we examined the properties of saliva secreted during the local stress response induced by a half marathon (HM) using quantitative proteomic analysis.

Methods

The Exercise group (ExG), 19 healthy female university students participated in (HM) race. The non-exercise group (NExG), 16 healthy female university students had not participated in the ExG. In ExG, saliva samples were collected 1h pre and 2h and 4h post HM. NExG were collected in same time interval. Saliva volume, protein concentration and relative IGHA1 expression were analyzed. In addition, 1h pre and 2h post HM saliva were analyzed by iTRAQ. The identified factors of iTRAQ, analyzed for the ExG and NExG by western blotting.

Results

We identified kallikrein 1 (KLK1), immunoglobulin kappa chain (IgK) and cystatin S (CST4) as suppression factors, as well as immunoglobulin heavy constant alpha 1 (IGHA1), which has been reported as an immunological stress marker. KLK1 (p= 0.011), IGK (p= 0.002), and CST4 (p= 0.003) were suppressed 2 h post-HM compared to pre-HM, and KLK1 (p= 0.004) and CST4 (p= 0.006) were suppressed 4 h post-HM. There was also a positive correlation between IGHA1, IGK, and CST4 2 and 4 h post-HM. In addition, KLK1 and IGK after 2 h post-HM showed a positive correlation.

Conclusion

Our study demonstrated that the salivary proteome is regulated and antimicrobial proteins are suppressed post-HM. These results suggest that oral immunity was transiently suppressed post-HM. The positive correlation of each protein at 2 and 4 h post-HM suggests that the suppressed state was similarly regulated up to 4 h after a HM. The proteins identified in this study may have applications as stress markers for recreational runners and individuals who perform high- and moderate-intensity exercises in their daily lives.
Spatial mapping of posture-dependent resistance to passive displacement of the hypertonic arm post-stroke
Authors: Kanade-Mehta Priyanka , Bengtson Maria , Stoeckmann Tina , McGuire John , Ghez Claude , Scheidt Robert A
Published: November 2022

Muscles in the post-stroke arm commonly demonstrate abnormal reflexes that result in increased position- and velocity-dependent resistance to movement. We sought to develop a reliable way to quantify mechanical consequences of abnormal neuromuscular mechanisms throughout the reachable workspace in the hemiparetic arm post-stroke. Survivors of hemiparetic stroke (HS) and neurologically-intact (NI) control subjects were instructed to relax as a robotic device repositioned the hand of their (hemiparetic) arm between several testing locations sampling the arm’s passive range of motion. During transitions, the robot induced motions at either the shoulder or elbow joint at speeds ranging from very slow (6 °/s) to fast (90 °/s). The robot held the hand at the testing location for at least 20 seconds after each transition. We recorded and analyzed hand force and electromyographic activities from selected muscles spanning the shoulder and elbow during and after transitions. Hand forces and electromyographic activities were small at all speeds and sample times in NI control subjects, but varied systematically by transport speed during and shortly after movement in the HS subjects. Velocity-dependent resistance to stretch diminished within two seconds after movement ceased in the hemiparetic arms. Hand forces and EMGs changed very little from 2 seconds after the movement ended onward, exhibiting dependence on limb posture but no systematic dependence on movement speed or direction. Although each HS subject displayed a unique field of hand forces and EMG responses across the workspace after movement ceased, the magnitude of steady-state hand forces was generally greater near the outer boundaries of the workspace than in the center of the workspace for the HS group but not the NI group. In the HS group, electromyographic activities exhibited abnormalities consistent with stroke-related decreases in the stretch reflex thresholds post-stroke. These observations were consistent across repeated testing days. Implications of the findings are discussed.
Tradeoffs and Benefits Explain Scaling, Sex Differences, and Seasonal Oscillations in the Remarkable Weapons of Snapping Shrimp (Alpheus spp.)
Authors: Dinh Jason P. , Patek S.N.
Published: November 2022

Evolutionary theory suggests that individuals should express costly traits at a magnitude that optimizes the cost-benefit ratio for the trait-bearer. Trait expression varies across a species because costs and benefits vary among individuals. For example, if large individuals pay lower costs than small individuals, then larger individuals should reach optimal cost-benefit ratios at a greater magnitude of trait expression. Using the remarkable cavitation-shooting weapons found in the big claws of male and female alpheid snapping shrimp, we test whether size- and sex-dependent expenditures explain the scaling of weapon size relative to body size and why males have larger proportional weapon size than females. We found that males and females from three snapping shrimp species (Alpheus heterochaelis, Alpheus angulosus,andAlpheus estuariensis) exhibit resource allocation tradeoffs between weapon and abdomen mass. For maleA. heterochaelis, the species for which we had the greatest sample size and statistical power, the smallest individuals showed the steepest tradeoff. Our extensive dataset inA. heterochaelisalso included data about pairing, breeding season, and egg clutch size. Therefore, we could test for reproductive tradeoffs and benefits in this species. FemaleA. heterochaelisexhibited additional tradeoffs between weapon size and egg count, average egg volume, and total egg mass volume. For average egg volume, the smallest females exhibited the steepest tradeoff relative to weapon size. Furthermore, in males but not females, large weapons were positively correlated with the probability of being paired and the relative size of their pair mate. In conclusion, we establish that size-dependent tradeoffs underlie reliable scaling relationships of costly traits. Furthermore, we show that males and females differ in weapon investment, suggesting that weapons are especially beneficial to males and especially burdensome to females.
Latent factor in Brain RNA-seq studies reflects cell type and clinical heterogeneity
Authors: Al-Ouran Rami , Liu Chaozhong , Wang Linhua , Wan Ying-Wooi , Li Xiqi , Milosavljevic Aleksandar , Shulman Joshua M. , Liu Zhandong
Published: November 2022

With the growing availability of Alzheimer’s disease (AD) transcriptomic data, several studies have nominated new therapeutic targets. However, a major challenge is accounting for latent (hidden) factors which affect the discovery of therapeutic targets. Using unsupervised machine learning, we identified a latent factor in brain tissue, and we validated the factor in AD and normal samples, across multiple studies, and different brain tissues. Moreover, significant metabolic differences were observed due to the latent factor. The latent factor was found to reflect cell-type heterogeneity in the brain and after adjusting for it, we were able to identify new biological pathways. The changes observed at both transcriptomic and metabolomic levels support the importance of identifying any latent factors before pursuing downstream analysis to accurately identify biomarkers.
Association of Biological Age with Tumor Microenvironment in Patients with Esophageal Adenocarcinoma
Authors: Ravensbergen C.J. , Holstein Y. van , Hagenaars S.C. , Crobach A.S.L.P. , Trompet S. , Portielje J.E.A. , de Glas N.A. , van Heemst D. , van den Bos F. , Tollenaar R.A.E.M. , Mesker W.E. , Mooijaart S.P. , Slingerland M.
Published: November 2022

Biological age-related adaptations have been shown to modulate the non-malignant cells comprising the tumor microenvironment (TME). In the current work, we studied the association between biological age and TME characteristics in patients with esophageal adenocarcinoma. We comparatively assessed intratumoral histologic stroma quantity, tumor immune cell infiltrate, and blood leukocyte and thrombocyte count in 72 patients stratified in 3 strata of biological age (younger <70 years, fit older ≥70 years, and frail older adults ≥70 years), as defined by a geriatric assessment. Frailty in older adults was predictive of decreased intratumoral stroma quantity (B = -14.66% stroma,P= 0.022) relative to tumors in chronological-age-matched fit older adults. Moreover, in comparison to younger adults, frail older adults (P= 0.032), but not fit older adults (P= 0.302), demonstrated a lower blood thrombocyte count at the time of diagnosis. Lastly, we found an increased proportion of tumors with a histologic desert TME phenotype in frail older adults. Our findings provide a biological underpinning for the clinical relevance of assessing frailty in patients with esophageal adenocarcinoma, further justifying the need for standardized geriatric assessment in geriatric cancer patients.
Geographic Information System Protocol for Mapping Areas Targeted for Mosquito Control in North Carolina
Authors: Mueller Andrew , Thomas Anthony , Brown Jeff , Young Abram , Smith Kim , Connelly Roxanne , Richards Stephanie L.
Published: November 2022

Geographic information systems (GIS) can be used to map mosquito larval and adult habitats and human populations at risk for mosquito exposure and possible arbovirus transmission. GIS can help simplify and target mosquito control efforts during routine surveillance and post-disaster (e.g., hurricane-related flooding) to protect emergency workers and public health. A practical method for prioritizing areas for emergency mosquito control has been developed and is described here. North Carolina (NC) One Map was used to identify state-level data layers of interest based on human population distribution and mosquito habitat in Brunswick, Columbus, Onslow, and Robeson Counties in eastern NC. Relevant data layers were included to create mosquito control treatment areas for targeted control and an 18-step protocol for map development is discussed. This protocol is expected to help state, territorial, tribal, and/or local public health officials and associated mosquito control programs efficiently create treatment area maps to improve strategic planning in advance of a disaster. This protocol may be applied to any NC county and beyond, thereby increasing local disaster preparedness.
The Src and Abl family kinases activate the Spleen Tyrosine Kinase to maximize phagocytosis andLeishmaniainfection
Authors: Ullah Imran , Barrie Umaru , Kernen Rebecca M. , Mamula Emily T. , Khuong Francis Tho Huu , Booshehri Laela M. , Rhodes Emma L. , Bradford James M. , Datta Arani , Wetzel Dawn M.
Published: November 2022

Leishmaniaspp. are obligate intracellular parasites that must be internalized by phagocytic cells to evade immune responses and cause disease. The uptake of bothLeishmaniapromastigotes (insect-stage parasites) and amastigotes (proliferative stage parasites in humans and mice) by phagocytes is thought to be mainly host cell-driven, not parasite-driven. Our previous work indicates that host Src and Abl family kinases facilitateLeishmaniaentry into macrophages and pathogenesis in murine cutaneous leishmaniasis. Here we demonstrate that host spleen tyrosine kinase (SYK) is required for efficient uptake ofLeishmaniapromastigotes and amastigotes. A Src family kinase-Abl family kinase-SYK signaling cascade inducesLeishmaniaamastigote internalization. Finally, lesion size and parasite burden duringLeishmaniainfection is significantly decreased in mice lacking SYK in monocytes or by treatment with the SYK inhibitor entospletinib. In summary, SYK is required for maximalLeishmaniauptake by macrophages and disease in mice. Our results suggest potential for treating leishmaniasis using host cell-directed agents.

SUMMARY STATEMENT

Activation of Spleen Tyrosine Kinase by Src and Abl family kinases is required for maximalLeishmaniauptake by macrophages and disease in a mouse model of cutaneous leishmaniasis.
Exploration of Mechanisms of Drug Resistance in a Microfluidic Device and Patient Tissues
Authors: Lim Wanyoung , Hwang Inwoo , Zhang Jiande , Chen Zhenzhong , Han Jeonghun , Jeon Jaehyung , Koo Bon-Kyoung , Kim Sangmin , Lee Jeong Eon , Kim Youngkwan , Pienta Kenneth J. , Amend Sarah R. , Austin Robert H. , Ahn Jee-Yin , Park Sungsu
Published: November 2022

Chemoresistance is a major cause of treatment failure in many cancers. However, the life cycle of cancer cells as they respond to and survive environmental and therapeutic stress is understudied. In this study, we utilized a microfluidic device to induce the development of doxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11 days by generating gradients of DOX and medium.In vivochemoresistant xenograft models, an unbiased genome-wide transcriptome analysis, and a patient data/tissue analysis all showed that chemoresistance arose from failed epigenetic control of the nuclear protein-1 (NUPR1)/histone deacetylase 11 (HDAC11) axis, and highNupr1expression correlated with poor clinical outcomes. These results suggest that the chip can rapidly induce resistant cells that increase tumor heterogeneity and chemoresistance, highlighting the need for further studies on the epigenetic control of the NUPR1/HDAC11 axis in TNBC.
A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics
Authors: Liu Liang , Sun Peiqing , Zhang Wei
Published: November 2022

mRNA cleavage and polyadenylation is an integral 2-step process in the generation of protein-encoding mRNA or noncoding transcripts. More than 60% of human genes have multiple polyadenylation sites either in the 3’ untranslated region (3’UTR-APA) or in the intronic/exonic region, resulting in expression of isoforms with alternative polyadenylation (APA) under different physiologic conditions. The 3’UTR-APAs have been extensively studied, but the biology of intronic polyadenylations (IPA) remain largely unexplored. Here we characterized the IPA profiles of 9,679 patient samples across 32 cancer types from the Cancer Genome Atlas (TCGA) cohort. Overall, we identified 22,260 detectable IPA sites; 9,014 (40.5%) occurred in all 32 cancer types and 11,676 (52.5%) occurred in 2 to 31 cancer types. By comparing tumors and their paired normal tissues, we identified 180 to 4,645 dysregulated IPAs in 132 to 2,249 genes in each of 690 patient tumors from 22 cancer types that showed consistent patterns within individual cancer types. Furthermore, across all cancer types, IPA isoforms and their gene regulation showed consistent pan-cancer patterns, and cancer types with similar histologic features were clustered at higher levels of hierarchy. We selected 2,741 genes that were consistently regulated by IPAs across cancer types, including 1,834 pan-cancer tumor-enriched and 907 tumor-depleted IPA genes. Pan-cancer tumor-enriched IPA genes were amply represented in the functional pathways such as cilium assembly and DNA damage repair. Expression of IPA isoforms in DNA damage repair genes was associated with tumor mutation burdens. Expression of IPA isoforms of tumor-enriched IPA genes was also associated with patient characteristics (e.g., sex, race, cancer stages, and subtypes) in cancer-specific and feature-specific manners. Importantly, IPA isoform expression for some genes could be a more accurate prognostic marker than gene expression (summary of all possible isoforms). In summary, our study reveals the roles and the clinical relevance of tumor-associated IPAs in cancer.
CREPE: A Shiny App for Transcription Factor Cataloguing
Authors: Rosado-Tristani Diego A. , Rodríguez-Martínez José A.
Published: November 2022

Transcription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unravelling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE was benchmarked against curated human transcription factor datasets. Next, we use CREPE to explore the TF repertoires ofHeliconius erato and Heliconius melpomenebutterflies. CREPE is available as a Shiny app package available at GitHub (github.com/dirostri/CREPE).
A transcriptional response to replication stress selectively expands a subset ofBRCA2-mutant mammary epithelial cells
Authors: Najafabadi Maryam Ghaderi , Gray G. Kenneth , Kong Li Ren , Gupta Komal , Perera David , Brugge Joan , Venkitaraman Ashok , Shehata Mona
Published: November 2022

BRCA2 mutation carriers preferentially develop luminal-like breast cancers, but it remains unclear how BRCA2 mutations affect mammary epithelial subpopulations. Here, we report that Brca2mut/WTmammary organoids subjected to replication stress activated a transcriptional response that selectively expands Brca2mut/WTluminal cells lacking hormone receptor expression (HR-). While CyTOF analyses revealed comparable epithelial compositions among wildtype and Brca2mut/WTmammary glands, Brca2mut/WTHR- luminal cells exhibited greater organoid formation and preferentially survived and expanded under replication stress. ScRNA-seq analysis corroborated the expansion of HR- luminal cells which express elevated levels of Tetraspanin-8 (Tspan8) andThrspmRNA, and pathways implicated in replication stress survival including Type I interferon responses. Notably, CRISPR/Cas9-mediated deletion ofTspan8orThrspprevented Brca2mut/WTHR- luminal cell expansion. Our findings indicate that Brca2mut/WTcells have an activate a transcriptional response after replication stress that preferentially favours outgrowth of HR- luminal cells through the expression of interferon-responsive and mammary alveolar genes.
A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing drugs in RB1-deficient ovarian and breast cancer cells
Authors: Bulanova Daria , Akimov Yevhen , Senkowski Wojciech , Oikkonen Jaana , Gall-Mas Laura , Timonen Sanna , Elmadani Manar , Hynninen Johanna , Hautaniemi Sampsa , Aittokallio Tero , Wennerberg Krister
Published: November 2022

Treatment of patients with high-grade serous ovarian carcinoma (HGSOC) and triple-negative breast cancer (TNBC) includes platinum-based drugs, gemcitabine, and PARP inhibitors. However, resistance to these therapies develops in most cases, highlighting the need for novel therapeutic approaches and biomarkers to guide the optimal treatment choice. Using a CRISPR loss-of-function screen for carboplatin sensitizers in the HGSOC cell line OVCAR8, we identifiedCSNK2A2, the gene encoding for the alpha’ (α’) catalytic subunit of casein kinase 2 (CK2). Expanding on this finding, we confirmed that the CK2 inhibitors silmitasertib and SGC-CK2-1 sensitized many, but not all, TNBC and HGSOC cell lines to the drugs that perturb DNA replication, including platinum drugs, gemcitabine, and PARP inhibitors. We identified RB1 tumor suppressor deficiency as a prerequisite context for the CK2 inhibition-mediated sensitization to these therapeutics. In RB1-deficient cells, CK2 inhibition resulted in accumulation of cells in S phase of the cell cycle, associated with micronuclei formation, and accelerated PARP inhibitor-induced aneuploidy and mitotic cell death. Patient HGSOC organoids that lacked RB1 expression displayed an enhanced long-term response to carboplatin and PARP inhibitor niraparib when combined with silmitasertib, suggesting RB1-stratified efficacy in patients. As RB1 deficiency affects up to 25% of HGSOC and 40% of TNBC cases, CK2 inhibition, proven safe from previous clinical exploration with silmitasertib, is a promising approach to overcome resistance to standard therapeutics in large strata of patients.
Rational strain design with minimal phenotype perturbation
Authors: Narayanan Bharath , Weilandt Daniel , Masid Maria , Miskovic Ljubisa , Hatzimanikatis Vassily
Published: November 2022

Increased availability of multi-omics data has facilitated the characterization of metabolic phenotypes of cellular organisms. However, devising genetic interventions that drive cellular organisms toward the desired phenotype remains challenging in terms of time, cost, and resources. Kinetic models, in particular, hold great potential for accelerating this task since they can simulate the metabolic responses to environmental and genetic perturbations. Although the challenges in building kinetic models have been well-documented, there exists no consensus on how to use these models for strain design in a computationally tractable manner. A straightforward approach that exhaustively simulates and evaluates putative designs would be impractical, considering the intensive computational requirements when targeting multiple enzymes. We address this issue by introducing a framework to efficiently scout the space of designs while respecting the physiological requirements of the cell. The framework employs mixed-integer linear programming and nonlinear simulations with large-scale nonlinear kinetic models to devise genetic interventions in a scalable manner while accounting for the network effects of these perturbations. More importantly, the framework ensures the engineered strain’s robustness by maintaining its phenotype close to that of the reference strain. We use the framework to improve the production of anthranilate, a precursor for pharmaceutical drugs, inE. coli. The devised strategies include eight previously experimentally validated targets and also novel designs suitable for experimental implementation. As an essential part of the future design-build-test-learn cycles, we anticipate that this novel framework will enable high throughput designs and accelerated turnover in biotechnological processes.