Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics.

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNA in situ hybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope-a recently developed novel technology-repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

A Greater Platelet Dose May Yield Better Clinical Outcomes for Platelet-Rich Plasma in the Treatment of Knee Osteoarthritis: A Systematic Review.

PURPOSE: To determine whether the platelet dose administered during a platelet-rich plasma (PRP) injection for knee osteoarthritis (OA) affects clinical outcomes. METHODS: A systematic review was performed by searching PubMed, Cochrane Library, and Embase for randomized controlled trials with at least 1 study arm using PRP for knee OA. Only studies that provided a platelet count, concentration, or dose with a minimum of 6-month outcome scores were included. Studies in which the PRP group had statistically significant positive outcomes were separated from those without statistical significance. The average platelet doses for studies with positive outcomes in the PRP group were compared with those without positive outcomes. RESULTS: After exclusion criteria were applied, 29 studies were analyzed. Of the 29, there were 31 arms that used PRP as a treatment method, of which 28 had statistically significant positive outcomes at 6 months compared with the control group. The mean platelet dose in the 28 with a positive outcome was 5,500 ± 474 × 106, whereas the 3 that had no positive difference had a mean platelet dose of 2,302 ± 437 × 106 (P < .01). There were 18 studies with 12-month outcomes, with 16 of 18 having positive outcomes. The positive studies had an average platelet dose of 5,464 ± 511, whereas the studies that had no statistical difference had an average platelet dose of 2,253 ± 753 × 106 (P < .05). CONCLUSIONS: Improved clinical outcomes from PRP injections for knee OA may be related to a greater platelet dose. LEVEL OF EVIDENCE: Level II, systematic review of Level I and II studies.

Entrepreneurship and Criminal Justice Populations: A Social Cognitive Perspective.

A criminal record limits employment opportunities of those released from prison. Entrepreneurship, or starting one's own business venture, has been suggested as a way to overcome the employment barriers of a criminal record, given that many justice-involved persons have entrepreneurship experiences, often through illegal ventures. Sparse research has investigated how legal or illegal business experience translates to legal entrepreneurship attitudes. Using social cognitive career theory-career theory (SCCT), and concepts from the Risk Need Responsivity (RNR) model, the role of illegal and legal business exposure were investigated. Findings indicated that both legal and illegal business exposure had a positive influence on entrepreneurship goals through entrepreneurship self-efficacy and entrepreneurship outcome expectations. Legal experiences had a stronger influence. Criminal thinking, a significant risk factor for return to criminal behavior, was investigated in its role in entrepreneurship attitudes. Findings indicated that criminal thinking had an indirect effect on entrepreneurship goals through entrepreneurship self-efficacy.

Machine learning models predict PTSD severity and functional impairment: A personalized medicine approach for uncovering complex associations among heterogeneous symptom profiles.

OBJECTIVE: Posttraumatic stress disorder (PTSD) is a debilitating psychiatric illness, experienced by approximately 10% of the population. Heterogeneous presentations that include heightened dissociation, comorbid anxiety and depression, and emotion dysregulation contribute to the severity of PTSD, in turn, creating barriers to recovery. There is an urgent need to use data-driven approaches to better characterize complex psychiatric presentations with the aim of improving treatment outcomes. We sought to determine if machine learning models could predict PTSD-related illness in a real-world treatment-seeking population using self-report clinical data. METHOD: Secondary clinical data from 2017 to 2019 included pretreatment measures such as trauma-related symptoms, other mental health symptoms, functional impairment, and demographic information from adults admitted to an inpatient unit for PTSD in Canada (n = 393). We trained two nonlinear machine learning models (extremely randomized trees) to identify predictors of (a) PTSD symptom severity and (b) functional impairment. We assessed model performance based on predictions in novel subsets of patients. RESULTS: Approximately 43% of the variance in PTSD symptom severity (R²avg = .43, R²median = .44, p = .001) was predicted by symptoms of anxiety, dissociation, depression, negative trauma-related beliefs about others, and emotion dysregulation. In addition, 32% of the variance in functional impairment scores (R²avg = .32, R²median = .33, p = .001) was predicted by anxiety, PTSD symptom severity, cognitive dysfunction, dissociation, and depressive symptoms. CONCLUSIONS: Our results reinforce that dissociation, cooccurring anxiety and depressive symptoms, maladaptive trauma appraisals, cognitive dysfunction, and emotion dysregulation are critical targets for trauma-related interventions. Machine learning models can inform personalized medicine approaches to maximize trauma recovery in real-world inpatient populations. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Correction: Evolution and consequences of individual responses during the COVID-19 outbreak.

[This corrects the article DOI: 10.1371/journal.pone.0273964.].

Nurse-Driven Interprofessional Rounds: Improving Care Coordination and Length of Stay.

BACKGROUND: Inpatient oncology units care for patients with some of the most complex medical conditions outside of the intensive care unit. These patients benefit from structured care coordination. Reduced ability to admit patients to oncology beds contributes to delays in specialty care. OBJECTIVES: This quality improvement initiative established nurse-driven interprofessional rounds (IPRs) to reduce length of stay (LOS), improve discharge time of day, and enhance care coordination, patient flow, and access to care in the community. METHODS: Care coordination during enhanced IPRs (eIPRs) included estimation of discharge dates, comparison of LOS to a standard geometric mean LOS, and discussion of clinical milestones and barriers to progression and discharge. Data analysis evaluated the effect of eIPRs on key outcomes. FINDINGS: Although LOS variance was reduced by 15.8% and 44.1% in all-unit and hematology-oncology discharges, respectively, the results were not significant. Discharges by 2 pm improved significantly for all-unit and hematology-oncology populations, respectively. Patient flow measured by accepted patient transfers requesting hematology-oncology services improved significantly.

The role of civil society organizations (CSOs) in the COVID-19 response across the Global South: A multinational, qualitative study.

Despite receiving less attention than high-income countries, low- and middle-income countries (LMICs) experienced more than 85% of global excess deaths during the first two years of the COVID-19 pandemic. Due to the unprecedented speed and scale of the COVID-19 pandemic, which placed large demands on government capacity, many LMICs relied on civil society organizations (CSOs) to assist in implementing COVID-19 response programs. Yet few studies have examined the critical role CSOs played in mitigating the effects of the COVID-19 pandemic in low resource settings. This study explored the CSO response to COVID-19 in five of the most heavily impacted LMICs in the Global South. Interviews were conducted from May to August 2021 with a purposive sample of CSO key informants within each of the five countries. A total of 52 CSOs were selected from which 53 key informants were interviewed either via Zoom or by phone. Interviews were coded and analyzed using NVivo or MAXQDA2020. Out of the 52 CSOs selected, 24 were national organizations, 8 were regional, and 20 were local. CSOs fell into six categories: community-based organizations, non-governmental organizations, unions/professional organizations, campaigns/social movements, research organizations/think tanks, and networks/coalitions. CSOs across all five countries adapted their missions, stretched their resources, and performed a wide range of activities that fit into five programmatic areas: food security and livelihood support, public health and medical care, cash transfer programs, risk communication and community education, and needs assessment. This qualitative analysis demonstrates the critical role CSOs played in supplementing government emergency aid response by delivering necessary resources and supporting highly vulnerable populations during the COVID-19 pandemic, as well as the primary challenges they faced in doing so. Given the generally weak state of public capacity in the LMICs studied, this role was vital to responding to the pandemic.

Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice.

Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Mitochondrial uncoupling protein 1 (UCP1) is activated in BAT during cold stress and dissipates mitochondrial proton motive force generated by the electron transport chain to generate heat. However, other mitochondrial factors required for brown adipocyte respiration and thermogenesis under cold stress are largely unknown. Here, we show LETM1 domain-containing protein 1 (LETMD1) is a BAT-enriched and cold-induced protein required for cold-stimulated respiration and thermogenesis of BAT. Proximity labeling studies reveal that LETMD1 is a mitochondrial matrix protein. Letmd1 knockout male mice display aberrant BAT mitochondria and fail to carry out adaptive thermogenesis under cold stress. Letmd1 knockout BAT is deficient in oxidative phosphorylation (OXPHOS) complex proteins and has impaired mitochondrial respiration. In addition, BAT-specific Letmd1 deficient mice exhibit phenotypes identical to those observed in Letmd1 knockout mice. Collectively, we demonstrate that the BAT-enriched mitochondrial matrix protein LETMD1 plays a tissue-autonomous role that is essential for BAT mitochondrial function and thermogenesis.

Surface ID: a geometry-aware system for protein molecular surface comparison.

MOTIVATION: A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein's function such as its ability to interact with other molecules. While many methods have been developed for comparing the similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited. RESULTS: Here, we describe "Surface ID," a geometric deep learning system for high-throughput surface comparison based on geometric and chemical features. Surface ID offers a novel grouping and alignment algorithm useful for clustering proteins by function, visualization, and in silico screening of potential binding partners to a target molecule. Our method demonstrates top performance in surface similarity assessment, indicating great potential for protein functional annotation, a major need in protein engineering and therapeutic design. AVAILABILITY AND IMPLEMENTATION: Source code for the Surface ID model, trained weights, and inference script are available at https://github.com/Sanofi-Public/LMR-SurfaceID.

Intermittent Fasting Activates AMP-Kinase to Restructure Right Ventricular Lipid Metabolism and Microtubules.

Intermittent fasting (IF) extends life span via pleotropic mechanisms, but one important molecular mediator is adenosine monophosphate-activated protein kinase (AMPK). AMPK enhances lipid metabolism and modulates microtubule dynamics. Dysregulation of these molecular pathways causes right ventricular (RV) failure in patients with pulmonary arterial hypertension. In rodent pulmonary arterial hypertension, IF activates RV AMPK, which restores mitochondrial and peroxisomal morphology and restructures mitochondrial and peroxisomal lipid metabolism protein regulation. In addition, IF increases electron transport chain protein abundance and activity in the right ventricle. Echocardiographic and hemodynamic measures of RV function are positively associated with fatty acid oxidation and electron transport chain protein levels. IF also combats heightened microtubule density, which normalizes transverse tubule structure.

Mental Health and Involuntary Retirement from Sports Post-Musculoskeletal Injury in Adult Athletes: a Systematic Review.

PURPOSE OF REVIEW: The psychological aspects of musculoskeletal injury are often overlooked in the rehabilitation process. This review examines the effects of musculoskeletal injury on mental health in adult athletes and identifies themes to guide further research. RECENT FINDINGS: Athletes are at risk for mental health struggles due to high athletic identity and identity foreclosure. Injured athletes have specifically been shown to have higher rates of anxiety and depression when compared to the general population. There is a lack of intervention-based research on the psychological well-being of athletes, and there are no systematic reviews synthesizing the impact of musculoskeletal injury on the mental health of adult athletes across a variety of sports. Across professional, college-level, and amateur athletes, musculoskeletal injury is associated with worse mental health scores, including higher distress, higher anxiety and depression, lower social functioning, and lower health-related quality of life. For adults, involuntary retirement from sports due to musculoskeletal injury is a common theme associated with increased psychological distress, anxiety, and depression. In the reviewed literature, 22 unique mental health and 12 distinct physical health screening tools were used. Two articles studied interventions addressing mental health post-injury. Further research using an integrated physical and psychological approach to recovery is warranted and may improve mental and physical outcomes for injured athletes.

Mechanistic incorporation of FcRn binding in plasma and endosomes in a whole body PBPK model for large molecules.

Monoclonal antibodies, endogenous IgG, and serum albumin bind to FcRn in the endosome for salvaging and recycling after pinocytotic uptake, which prolongs their half-life. This mechanism has been broadly recognized and is incorporated in currently available PBPK models. Newer types of large molecules have been designed and developed, which also bind to FcRn in the plasma space for various mechanistic reasons. To incorporate FcRn binding affinity in PBPK models, binding in the plasma space and subsequent internalisation into the endosome needs to be explicitly represented. This study investigates the large molecules model in PK-Sim® and its applicability to molecules with FcRn binding affinity in plasma. With this purpose, simulations of biologicals with and without plasma binding to FcRn were performed with the large molecule model in PK-Sim®. Subsequently, this model was extended to ensure a more mechanistic description of the internalisation of FcRn and the FcRn-drug complexes. Finally, the newly developed model was used in simulations to explore the sensitivity for FcRn binding in the plasma space, and it was fitted to an in vivo dataset of wild-type IgG and FcRn inhibitor plasma concentrations in Tg32 mice. The extended model demonstrated a strongly increased sensitivity of the terminal half-life towards the plasma FcRn binding affinity and could successfully fit the in vivo dataset in Tg32 mice with meaningful parameter estimates.

Stronger Athlete Identity Is a Risk Factor for More Severe Depressive Symptoms After Musculoskeletal Injury in Pediatric Athletes: a Systematic Review.

PURPOSE OF REVIEW: Treatment for musculoskeletal sports injuries often neglects the psychological components of health and recovery. Pediatric patients require particular consideration of their psychosocial and cognitive development. This systematic review investigates the effects of musculoskeletal injury on mental health in pediatric athletes. RECENT FINDINGS: Athlete identity may increase in adolescence and is associated with worse mental health post-injury. Psychological models suggest loss of identity, uncertainty, and fear mediate the association between injury and symptoms of anxiety, depression, post-traumatic stress disorder, and obsessive-compulsive disorder. Fear, identity, and uncertainty also influence return to sport. In the reviewed literature, there were 19 psychological screening tools and 8 different physical health measures with various adaptations to athlete developmental level. In pediatric patients, no interventions were studied to reduce the psychosocial impacts of injury. Musculoskeletal injury is associated with worse mental health in pediatric athletes, and stronger athlete identity is a risk factor for the development of depressive symptoms. Psychological interventions that reduce uncertainty and address fear may help mitigate these risks. More research is needed on screening and interventions to improve mental health post-injury.

Evolution and consequences of individual responses during the COVID-19 outbreak.

In a long-lasting major disease outbreak such as that of COVID-19, the challenge for public health authorities is to keep people motivated and keen on following safety guidelines. In this study, a compartmental model with a heterogeneous transmission rate (based on awareness) is utilized to hypothesize about the public adoption of preventive guidelines. Three subsequent outbreaks in South Korea, Pakistan, and Japan were analyzed as case studies. The transmission, behavior change, and behavioral change ease rates of the disease were measured in these countries. The parameters were estimated using the maximum likelihood method with an additional identifiability analysis performed to determine the uniqueness of the estimated parameters for quantitatively comparing them during the first three waves of COVID-19. The mathematical analysis and simulation results show that individual responses had a significant effect on the outbreak. Individuals declining to follow the public health guidelines in Korea and Japan between the second and third waves contributed to making the third peak the highest of the three peaks. In Pakistan, however, individual responses to following public health guidelines were maintained between the second and third waves, resulting in the third peak being lower than the first, rather than being associated with the highest transmission rate. Thus, maintaining a high level of awareness is critical for containing the spread. Improvised public health campaigns are recommended to sustain individual attention and maintain a high level of awareness.

Willingness to work among males on parole: A quantitative and qualitative analysis.

This study investigated employment attitudes of adult males who were recently released from prison and onto parole. The study investigated the role of willingness to work entry-level jobs, an understudied variable in career development of justice-involved persons. We hypothesized that criminal thinking and perception of barriers would each have a direct effect on job search self-efficacy and a direct and indirect effect on willingness to work entry-level jobs, through job search self-efficacy. We also predicted that criminal thinking and perception of barriers would each have an indirect effect on career aspirations within a job, through job search self-efficacy and willingness to work entry-level jobs. Results confirmed these hypotheses. Results of two serial mediation analyses indicated that perceiving more barriers to work predicted less job search self-efficacy, less job search self-efficacy predicted less willingness to work entry-level jobs, and less willingness to work entry-level jobs predicted lower career aspirations. Similarly, higher reactive criminal thinking predicted less job search self-efficacy, less job search self-efficacy predicted less willingness to work entry-level jobs, and less willingness to work entry-level jobs predicted lower career aspirations. Results of qualitative analysis indicated that the vast majority of parolees planned to work in entry-level jobs within the first few months of release from prison. The study sheds light on the work attitudes of males who leave prison and what factors may influence their willingness to work entry-level jobs. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Glycogen Storage Disease Phenotypes Accompanying the Perturbation of the Methionine Cycle in NDRG3-Deficient Mouse Livers.

N-Myc downstream regulated gene 3 (NDRG3) is a unique pro-tumorigenic member among NDRG family genes, mediating growth signals. Here, we investigated the pathophysiological roles of NDRG3 in relation to cell metabolism by disrupting its functions in liver. Mice with liver-specific KO of NDRG3 (Ndrg3 LKO) exhibited glycogen storage disease (GSD) phenotypes including excessive hepatic glycogen accumulation, hypoglycemia, elevated liver triglyceride content, and several signs of liver injury. They suffered from impaired hepatic glucose homeostasis, due to the suppression of fasting-associated glycogenolysis and gluconeogenesis. Consistently, the expression of glycogen phosphorylase (PYGL) and glucose-6-phosphate transporter (G6PT) was significantly down-regulated in an Ndrg3 LKO-dependent manner. Transcriptomic and metabolomic analyses revealed that NDRG3 depletion significantly perturbed the methionine cycle, redirecting its flux towards branch pathways to upregulate several metabolites known to have hepatoprotective functions. Mechanistically, Ndrg3 LKO-dependent downregulation of glycine N-methyltransferase in the methionine cycle and the resultant elevation of the S-adenosylmethionine level appears to play a critical role in the restructuring of the methionine metabolism, eventually leading to the manifestation of GSD phenotypes in Ndrg3 LKO mice. Our results indicate that NDRG3 is required for the homeostasis of liver cell metabolism upstream of the glucose-glycogen flux and methionine cycle and suggest therapeutic values for regulating NDRG3 in disorders with malfunctions in these pathways.

Accuracy of the Breast Cancer Surveillance Consortium Model Among Women with LCIS.

PURPOSE: The Breast Cancer Surveillance Consortium (BCSC) model predicts risk of invasive breast cancer risk based on age, race, family history, breast density, and history of benign breast disease, including lobular carcinoma in situ (LCIS). However, validation studies for this model included few women with LCIS. We sought to evaluate the accuracy of the BCSC model among this cohort. METHODS: Women with LCIS diagnosed between 1983 and 2017 were identified from a prospectively maintained database. The BCSC score was calculated; those with prior breast cancer, unknown breast density, age < 35 years or > 74 years, or with history of chemoprevention use were excluded. The Kaplan-Meier method was used to estimate incidence rates. Time-dependent receiver operating characteristic (ROC) analysis was used to analyze the discriminative capacity of the model. RESULTS: 1302 women with LCIS were included. At a median follow-up of 7 years, 152 women (12%) developed invasive cancer (6 with bilateral disease). Cumulative incidences of invasive breast cancer were 7.1% (95% CI 5.6-8.7) and 13.3% (95% CI 10.9-15.6), respectively, and the median BCSC risk scores were 4.9 and 10.4, respectively, at 5 and 10 years. The median 10-year BCSC score was significantly lower than the 10-year Tyrer-Cuzick score (10.4 vs 20.8, p < 0.001). The ROC curve scores (AUC) for BCSC at 5 and 10 years were 0.59 (95% CI 0.52-0.66) and 0.58 (95% CI 0.52-0.64), respectively. CONCLUSION: The BCSC model has moderate accuracy in predicting invasive breast cancer risk among women with LCIS with fair discrimination for risk prediction between individuals.

Atypical jobs in psychology: An interview with Dr. McCarthy.

This article summarizes the career of Dr. McCarthy, who is Dean of the College of Sciences and Humanities at Ball State University. She came from humble roots as the oldest of 10 children and is therefore grateful she was able to attend college. That experience gave her insight into the possible challenges of those pursuing a degree in higher education. This, coupled with her education in psychology, has helped her passionately serve both her students and faculty members in several public service roles, including her current position as dean. Through this interview, Dr. McCarthy was able to describe her background training, daily tasks, and the strategies she employs to effectively spark change at both the individual and institutional levels. She also discussed the rewards and challenges of her career. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Synchronous and metachronous bilateral breast cancer among women with a history of lobular carcinoma in situ.

PURPOSE: Lobular carcinoma in situ (LCIS) confers increased cancer risk in either breast, but it remains unclear if this population is at increased risk for bilateral breast cancer (BC) development. Here we report bilateral BC incidence among women with a history of LCIS. METHODS: Women with classic-type LCIS diagnosed from 1980 to 2017 who developed unilateral BC (UBC) or bilateral BC were identified. Bilateral BC was categorized as synchronous (bilateral BC diagnosed < 6 months apart; SBBC) or metachronous (bilateral BC diagnosed ≥ 6 months apart; MBBC). Five-year incidence rates of bilateral BC among this population were evaluated. Comparisons were made to identify factors associated with bilateral BC. RESULTS: At 7 years' median follow-up, 249/1651 (15%) women with LCIS developed BC; 34 with bilateral BC (2%). There were no clinicopathologic feature differences between those with UBC and bilateral BC. SBBC occurred in 18 without significant differences versus UBC. Among 211 with UBC and a contralateral breast at risk, 16 developed MBBC at a median follow-up of 3 years. MBBC patients were less likely to receive endocrine therapy and more likely to receive chemotherapy versus UBC. Tumor histology was not associated with MBBC. Estimated 5-year MBBC risk was 6.4%. Index estrogen/progesterone receptor positivity and endocrine therapy were the only factors associated with MBBC risk. CONCLUSION: Bilateral BC occurred in 2% of women with LCIS history at median follow-up of 7 years. Similar to the general BC population, a decrease in MBBC is seen among women with a history of LCIS who develop hormone receptor-positive disease and those who receive endocrine therapy, highlighting the protective effects of this treatment.