bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comprehensive conceptual and computational dynamics framework for autonomous regeneration of form and function in biological organisms
Authors: Samarasinghe Sandhya , Minh-Thai Tran Nguyen
Published: January 2023

In biology, regeneration is a mysterious phenomenon that has inspired self-repairing systems, robots, and biobots. It is a collective computational process whereby cells communicate to achieve an anatomical set point and restore original function in regenerated tissue or the whole organism. Despite decades of research, the mechanisms involved in this process are still poorly understood. Likewise, the current algorithms are insufficient to overcome this knowledge barrier and enable advances in regenerative medicine, synthetic biology, and living machines/biobots. We propose a comprehensive conceptual framework for the engine of regeneration with hypotheses for the mechanisms and algorithms of stem cell-mediated regeneration that enables a system like the planarian flatworm to fully restore anatomical (form) and bioelectric (function) homeostasis from any small- or large-scale damage. The framework extends the available regeneration knowledge with novel hypotheses to propose collective intelligent self-repair machines with multi-level feedback neural control systems driven by somatic and stem cells. We computationally implemented the framework to demonstrate the robust recovery of both form and function (anatomical and bioelectric homeostasis) in an in silico worm that, in a simple way, resembles the planarian. In the absence of complete regeneration knowledge, the framework contributes to understanding and generating hypotheses for stem cell mediated form and function regeneration, which may help advance regenerative medicine and synthetic biology. Further, as our framework is a bio-inspired and bio-computing self-repair machine, it may be useful for building self-repair robots/biobots and artificial self-repair systems.
A framework for residents’ pursuit of excellence based upon non-cognitive and cognitive attributes
Authors: Saxena Anurag , Desanghere Loni
Published: January 2023

Purpose

Excellence, although variably conceptualized, is commonly used in medicine and the resident excellence literature is limited. Both cognitive attributes (CAs) and non-cognitive attributes (NCAs) are essential for academic and clinical performance; however, the latter are difficult to evaluate. Undergirded by an inclusive and non-competitive approach and utilizing CAs and NCAs, we propose a criterion-referenced behavioral framework of resident excellence.

Methods

Perceptions of multiple stakeholders (educational administrators, faculty, and residents), gathered by survey (n = 218), document analysis (n = 52), and focus group (n = 23), were analyzed. Inductive thematic analysis was followed by deductive interpretation and categorization using sensitizing concepts for excellence, NCAs, and CAs. Chi-squared tests were used to determine stakeholder perception differences.

Results

All stakeholders had similar perceptions (P > .05) and 13 behavioral attributes in 6 themes undergirded by insight and conscientiousness were identified. The NCAs included: interpersonal skills (works with others, available, humble), professional (compassionate, trustworthy), commitment to profession (visible, volunteers), commitment to learn (proactively seeks feedback, creates learning opportunities), and work–life balance/integration (calm demeanor, inspirational). The CA (medical knowledge and intellect) included: applies knowledge to gain expertise and improves program’s caliber.

Conclusion

Resident excellence is posited as a pursuit. The attributes are non-competitive, inclusionary, potentially achievable by all, and do not negatively affect freedom of choice. However, contextual and cultural differences are likely and these need validation across societal equity segments. There are implications for learners (adaptive reflection and learning goal orientation), faculty (reduced bias and whole-person feedback), and system leaders (enhancing culture and learning environments) to foster excellence.
Emergency department claims among Medicare beneficiaries with HIV, STDs, viral hepatitis or tuberculosis before and during the COVID-19 pandemic
Authors: Chang Man-Huei , Moonesinghe Ramal , Truman Benedict I
Published: January 2023

Background

Changes in emergency department (ED) usage among US Medicare beneficiaries (MB) with fee-for-service claims for HIV, viral hepatitis, sexually transmitted diseases (STDs) or tuberculosis (TB) (HHST) services have not been assessed since the COVID-19 pandemic.

Methods

During 2006–20, we assessed the annual number of MB with each HHST per 1000 persons with ED claims for all conditions, and changes in demographic and geographic distribution of ED claimants for each HHST condition.

Results

Of all persons who attended an ED for any condition, 10.5 million (27.5%) were MB with ≥1 ED claim in 2006; that number (percentage) increased to 11.0 million (26.7%) in 2019 and decreased to 9.2 million (22.7%) in 2020; < 5 MB per 1000 ED population had HHST ED claims in 2020. The percentage increase in ED claims was higher for MB with STDs than for those with other HHST conditions, including a 10% decrease for MB with TB in 2020.

Conclusions

Trends in ED usage for HHST conditions were associated with changes in demographic and geographic distribution among MB during 2006–20. Updated ED reimbursement policies and primary care practices among MB might improve prevention, diagnosis and treatment of HHST conditions in the future.
The role of small GTPases in bisphenol AF-induced multinucleation in comparison with dibutyl phthalate in the male germ cells
Authors: Hu Chelin , Hsiao Zoey Hsuan , Yin Lei , Yu Xiaozhong
Published: January 2023

The goal of this study is to examine bisphenol AF (BPAF)-induced multinucleation (MNC) in comparison with dibutyl phthalate (DBP), known to induce MNC in mouse gonocytes in vivo. We performed image-based single-cell high content analysis (HCA) in the mouse spermatogonia C18-4 cells treated with various concentrations of BPAF and DBP. BPAF as low as 5 µM was cytotoxic and resulted in 40% cell death of the C18-4 cells after 72 h. HCA revealed that 5 µM of BPAF significantly increased the number of MNC by an average of 3.6-fold. DBP did not induce MNC in the doses we tested. Cytokinesis is tightly regulated by various small GTPase-signaling pathways. We, therefore, tested 5 selective GTPase inhibitors and found that Y27632, a ROCK inhibitor, reduced the BPAF-induced MNC by nearly 30%. Inhibition of Cdc42 by ML141 conversely increased the number of BPAF-induced MNC. We performed a hierarchical cluster analysis of the HCA data and demonstrated that the cytoskeletal disruption by BPAF was reversely modified by Y27632. We found that mRNA expression of genes regulating Rho and Rac GTPase activities, p190RhoGap and MgcRacGap, was altered in BPAF-treated C18-4 cells in a time-dependent manner. Multinucleated gonocytes are often indicators of disease pathologies. Our results provided the first evidence of mechanisms of the dual toxicity by BPAF to male germ cells, which induces chromosome endoreplication without the coordinated cytokinetic cellular components. The unique genotoxic mechanism of forming multinucleated germ cells suggests a novel mode of action in the male repro-toxicity concern over the increasingly ubiquitous presence of BPA analogs.
Next-generation PFAS 6:2 fluorotelomer sulfonate reduces plaque formation in exposed white-footed mice
Authors: Bohannon Meredith E , Narizzano Allison M , Guigni Blas A , East Andrew G , Quinn Michael J
Published: January 2023

6:2 fluorotelomer sulfonate (6:2 FTS) has been used as a replacement for legacy per- and polyfluoroalkyl substances (PFAS). We assessed reproductive and developmental effects in a human-wildlife hybrid animal model based on the association of adverse effects linked to legacy PFAS with these sensitive life stages. In this study, white-footed mice were exposed orally to 0, 0.2, 1, 5, or 25 mg/kg-day 6:2 FTS for 112 days (4 weeks premating exposure plus at least 4 weeks mating exposure). Pregnancy and fertility indices were calculated, and litter production, total litter size, live litter size, stillbirths, litter loss, average pup weight, and pinna unfolding were assessed. Sex steroid and thyroid hormone serum levels were assessed. Body weight, histopathology, and immune function were also assessed in this study. Reproductive endpoints were not significantly altered in response to 6:2 FTS. Spleen weight increased in male mice dosed with 6:2 FTS. Immune function determined via a plaque-forming cell (PFC) assay was decreased in both male and female mice in the 2 highest doses. A low benchmark dose was calculated based on PFCs as the critical effect and was found to be 2.63 and 2.26 mg/kg-day 6:2 FTS in male and female mice, respectively. This study characterizes 6:2 FTS as being potentially immunotoxic with little evidence of effect on reproduction and development; furthermore, it models acceptable levels of exposure. These 2 pieces of information together will aid regulators in setting environmental exposure limits for this PFAS currently thought to be less toxic than other PFAS.
A new recommendation for febrile urinary tract infection in children aged 2–24 months: Tepecik UTI Guideline-2
Authors: Koyun Cezayir Begüm , Yavascan Önder , Alaygut Demet , Demir Belde Kasap , Mutlubas Fatma , Arslansoyu Camlar Secil , Alparslan Caner , Soyaltin Eren , Ozgur Su
Published: January 2023

Aim

Urinary tract infections (UTIs) represent a common febrile illness in infancy. The study compared two UTI guidelines in terms of number of imaging studies, presence of parenchymal damage and radiation exposure in patients with the first febrile UTI between 2 and 24 months of age.

Method

The results of Tepecik UTI Guideline-1 used until 2012 (Group 1, n = 105) were retrospectively compared with Tepecik UTI Guideline-2 (Group 2) used after 2013. In Group 1, urinary tract ultrasonography (US), dimercaptosuccinic acid (DMSA) and voiding cystourethrography (VCUG) were made in all patients. In Group 2, if the US result was abnormal, patients were evaluated with VCUG and DMSA. If the US was normal, only DMSA was performed. If the DMSA was abnormal, the VCUG was undergone (n: 43, 40.9%).

Results

The abnormal VCUG detection rate was 69.2% in Group 1 and 30.8% in Group 2 (p = 0.09). Sensitivity and specificity of US in the diagnosis of vesicoureteral reflux (VUR) was 15.9% and 96.7% in Group 1 and 61.5% and 70.5% in Group 2, respectively. Abnormal DMSA findings were observed among 33.3% (Groups 1) and 66.7% (Groups 2) subjects, respectively (p > 0.05). The median radiation exposure (500 mrem) of patients in Group 1 was statistically significantly higher than those in Group 2 (200 mrem) (p < 0.001).

Conclusion

The VCUG should not be the first examination to be considered in such patients. We think that Tepecik UTI Guideline-2 reduces unnecessary invasive procedure and radiation exposure and not missed VUR in the management of children with UTI at 2–24 months. Needs prospective follow-up studies before considering this recommendation.
The right antibiotic for the right neonate? A prospective observational cohort study at a district hospital in Pemba, Tanzania
Authors: Larsen Lærke Vinge , Lassen Mathilde Languille , Lund Stine , Nygaard Ulrikka , Bech Christine Manich , Mzee Said , Ali Said Mouhammed , Poulsen Anja
Published: January 2023

Background

The highest neonatal mortality is in Sub-Saharan Africa, where neonatal sepsis accounts for approximately 50%. At Pemba Island, Tanzania, we examined the use of prophylactic antibiotics in neonates and related it to WHO guidelines and compared clinical signs of infection with the use of antibiotic treatment; furthermore, we aimed to investigate all use of antibiotic treatment in the neonatal period.

Method

This prospective observational cohort study was performed from 1 January 2022 to 15 April 2022 at a district hospital on Pemba Island, Tanzania. Women admitted in early established or active labour, and their neonates, were eligible for inclusion. We used questionnaires for mother and health worker and examined the neonates 2 h after birth. Follow-up was made at discharge or at 18 h of life, and days 7 and 28.

Results

We included 209 women and their 214 neonates. The neonatal mortality was 5 of 214 (23 per 1000 live births). According to WHO guidelines 29 (13.6%) had ≥ 1 risk factor for infection. Of these, three (10.3%) received prophylactic antibiotic treatment; only one (3.4%) received the correct antibiotic drug recommended in guidelines. Thirty-nine (18.2%) neonates had ≥ 1 clinical indicator of infection and 19 (48.7%) of these received antibiotic treatment. A total of 30 (14.0%) neonates received antibiotics during the study period. Twenty-three (76.7%) were treated with peroral antibiotics.

Conclusion

Adherence to WHO guidelines for prophylactic antibiotic treatment to prevent neonatal infection was low. Further, only half of neonates with clinical signs of infection received antibiotics.
Systemic C‐peptide supplementation ameliorates retinal neurodegeneration by inhibiting VEGF‐induced pathological events in diabetes
Authors: Lee Ah‐Jun , Moon Chan‐Hee , Lee Yeon‐Ju , Jeon Hye‐Yoon , Park Won Sun , Ha Kwon‐Soo
Published: January 2023

Diabetic retinopathy (DR) is caused by retinal vascular dysfunction and neurodegeneration. Intraocular delivery of C‐peptide has been shown to be beneficial against hyperglycemia‐induced microvascular leakage in the retina of diabetes; however, the effect of C‐peptide on diabetes‐induced retinal neurodegeneration remains unknown. Moreover, extraocular C‐peptide replacement therapy against DR to avoid various adverse effects caused by intravitreal injections has not been studied. Here, we demonstrate that systemic C‐peptide supplementation using osmotic pumps or biopolymer‐conjugated C‐peptide hydrogels ameliorates neurodegeneration by inhibiting vascular endothelial growth factor‐induced pathological events, but not hyperglycemia‐induced vascular endothelial growth factor expression, in the retinas of diabetic mice. C‐peptide inhibited hyperglycemia‐induced activation of macroglial and microglial cells, downregulation of glutamate aspartate transporter 1 expression, neuronal apoptosis, and histopathological changes by a mechanism involving reactive oxygen species generation in the retinas of diabetic mice, but transglutaminase 2, which is involved in retinal vascular leakage, is not associated with these pathological events. Overall, our findings suggest that systemic C‐peptide supplementation alleviates hyperglycemia‐induced retinal neurodegeneration by inhibiting a pathological mechanism, involving reactive oxygen species, but not transglutaminase 2, in diabetes.
Use of Nasal Swab Activity to Estimate Intake in Internal Dosimetry
Authors: Miller Guthrie , Dumit Sara , Poudel Deepesh , Klumpp John
Published: January 2023

In addition to a review of theoretical analyses, this work presents an empirical study of nasal swab data from the Los Alamos National Laboratory (LANL) database correlated with intake obtained from plutonium internal dosimetry calculations. As a result of this work, several “intake-versus-nasal-swab” models were derived. We advocate quantitative use of nasal swab measurements in dose assessment calculations and discuss ways that this can be done. The best description of the LANL plutonium internal dose database is arguably intake = A + Bx, where A = 2.7 Bq, B = 3.8, and x = summed nasal swab activity. The geometric standard deviation was found to be 8.2. This relationship, obtained using plutonium data, should apply also for other radionuclides.
Development of a structured musculoskeletal and rheumatic disease continuing education program for nurse practitioners
Authors: Kellahan Sara , Burnitt Lisa , Eisen Seth , Curtis Mary P. , Parks Deborah
Published: January 2023

The workforce shortage of musculoskeletal and rheumatic disease (MSK-RMD) trained providers has led to the need for additional education for nurse practitioners (NPs) in MSK-RMD. An educational certificate was developed and implemented collaboratively between an academic medical center and a college of nursing. The NP-focused MSK-RMD education program enhanced the assessment and treatment of a variety of common RSK-RMD conditions. Interviews and online surveys were conducted with participants to evaluate the program experience. Participant interviews and survey findings demonstrate overall NP satisfaction with the program. Expanding the program to create an accessible virtual continuing education course may improve accessibility of MSK-RMD education for NPs in primary care and multidisciplinary environments.
Patient-Related Factors Do Not Predict Use of Computer-Based Auditory Training by New Adult Cochlear Implant Recipients
Authors: Dornhoffer James R. , Kinkhabwala Corin M. , Chidarala Shreya , Ma Cheng , Schvartz-Leyzac Kara C. , Meyer Ted A. , Sterba Katherine R. , Dubno Judy R. , McRackan Theodore R.
Published: January 2023

Objective

The use of computer-based auditory training (CBAT) after cochlear implantation is associated with improved speech recognition and real-world functional abilities. However, patient-related factors associated with CBAT use remain unknown. This study seeks to identify such factors and recognize those at risk for not implementing CBAT.

Study Design

Prospective natural experiment.

Setting

Tertiary academic center.

Patients

A total of 117 new adult cochlear implant (CI) recipients with bilateral moderate-to-profound hearing loss.

Interventions/Main Outcome Measures

Patient demographic and lifestyle information, preimplantation aided speech recognition scores, Cochlear Implant Quality of Life (CIQOL) domain and global scores, CIQOL-Expectations scores, and CBAT use in the first 3 months after activation. Patient-related variables included age, sex, race, duration of hearing loss before implantation, hours of CI use per day, hearing-aid use before implantation, living arrangements/marital status, annual household income, employment, technology use, and education.

Results

Overall, 33 new CI users (28.2%) used CBAT in the first 3 months after activation. On bivariate analysis of the pre-CI CIQOL scores, CIQOL-Expectations score, aided speech recognition scores, and demographic/lifestyle factors examined, regular use of smartphone, tablet, or computer technology was significantly associated with an increased likelihood of CBAT use (odds ratio, 9.354 [1.198-73.020]), whereas higher CIQOL-Expectations emotional domain scores were associated with a lower likelihood of CBAT use (d = −0.69 [−1.34 to −0.05]). However, using multivariable analysis to control for potential confounding factors revealed no significant associations between CBAT use in the first 3 months after cochlear implantation and any examined factor.

Conclusions

No associations between patient demographic, lifestyle, or pre-CI speech recognition and patient-reported outcome measures and CBAT use were identified. Therefore, discussions with all patients after implantation on the availability of CBAT and its potential benefits are warranted. In addition, given the limited overall use of CBAT and its association with improved CI outcomes, future studies are needed to investigate facilitators and barriers to CBAT use.
Pipeline for Automated Processing of Clinical Cone-Beam Computed Tomography for Patient-Specific Temporal Bone Simulation: Validation and Clinical Feasibility
Authors: Andersen Steven Arild Wuyts , Hittle Brad , Keith Jason P. , Powell Kimerly A. , Wiet Gregory J.
Published: January 2023

Objective

Patient-specific simulation allows the surgeon to plan and rehearse the surgical approach ahead of time. Preoperative clinical imaging for this purpose requires time-consuming manual processing and segmentation of landmarks such as the facial nerve. We aimed to evaluate an automated pipeline with minimal manual interaction for processing clinical cone-beam computed tomography (CBCT) temporal bone imaging for patient-specific virtual reality (VR) simulation.

Study Design

Prospective image processing of retrospective imaging series.

Setting

Academic hospital.

Methods

Eleven CBCTs were selected based on quality and used for validation of the processing pipeline. A larger naturalistic sample of 36 CBCTs were obtained to explore parameters for successful processing and feasibility for patient-specific VR simulation.

Visual inspection and quantitative metrics were used to validate the accuracy of automated segmentation compared with manual segmentation. Range of acceptable rotational offsets and translation point selection variability were determined. Finally, feasibility in relation to image acquisition quality, processing time, and suitability for VR simulation was evaluated.

Results

The performance of automated segmentation was acceptable compared with manual segmentation as reflected in the quantitative metrics. Total time for processing for new data sets was on average 8.3 minutes per data set; of this, it was less than 30 seconds for manual steps. Two of the 36 data sets failed because of extreme rotational offset, but overall the registration routine was robust to rotation and manual selection of a translational reference point. Another seven data sets had successful automated segmentation but insufficient suitability for VR simulation.

Conclusion

Automated processing of CBCT imaging has potential for preoperative VR simulation but requires further refinement.
Labyrinthine Fluid Signal Intensity on T2-Weighted MR Imaging in Patients With Vestibular Schwannomas Undergoing Proton Radiotherapy: A Longitudinal Assessment
Authors: Koetsier Kimberley S. , Mehan William A. , Buch Karen , Welling D. Bradley , van Benthem Peter Paul G. , Hensen Erik F. , Shih Helen A.
Published: January 2023

Objective

In vestibular schwannoma patients, a loss of signal intensity (SI) on T2-weighted magnetic resonance imaging (MRI) has been reported within the ipsilateral labyrinth. The purpose of this study was to quantitatively evaluate the occurrence and course of this intensity loss in relation to proton radiotherapy and its possible association with hearing loss.

Study Design

Retrospective chart review.

Setting

Tertiary referral center.

Patients

Patients who received proton therapy for a vestibular schwannoma and underwent at least two high-resolution T2-weighted cisternographic sequence (constructive interference in steady state/fast imaging employing steady-state acquisition/DRIVE) MRIs and audiometry assessments.

Main Outcome Measures

Relative T2 SIs from the vestibules and basal/apical cochlear turns of the labyrinth, bilaterally.

Results

Ninety-five MRI scans from 34 patients were included. The apical turn of the ipsilateral cochlea showed a lower mean cochlear SI than on the contralateral side (±3.5 versus 5.0). The mean relative cochlear SI did not significantly change after proton radiotherapy. The ipsilateral vestibule showed a higher SI than the cochlea. The relative mean cochlear SI was not directly correlated to (the degree of) hearing loss before or after proton radiotherapy, nor did it predict future hearing loss.

Conclusion

The relative mean cochlear SI on cisternographic T2-MRI in vestibular schwannoma patients is diminished on the treated side, when compared with the ipsilateral vestibule and the contralateral cochlea/vestibule. The SI of the ipsilateral cochlea does not further decrease after proton radiotherapy and seems to be related to the tumor rather than the therapy. The diminished cochlear SI does not correlate with subsequent loss of hearing.
Predictive Ability of First-Side Cochlear Implant Performance in Adult Sequential Bilateral Cochlear Implantation
Authors: Quimby Alexandra E. , Wen Christopher Z. , Bigelow Douglas C. , Ruckenstein Michael J. , Brant Jason A.
Published: January 2023

Objective

Predictors of second-side cochlear implant performance have not been well studied. We sought to assess whether speech recognition scores from first-side cochlear implant (CI1) could predict second-side cochlear implant (CI2) scores in sequential bilaterally implanted adults.

Study Design

Retrospective review using a prospectively collected database.

Setting

Academic tertiary care hospital.

Patients

Fifty-seven adults with postimplantation speech recognition testing performed at least 12 months after CI2.

Intervention

Sequential bilateral CI.

Main Outcome Measures

CI2 performance at ≥12 months as measured using consonant–nucleus–consonant (CNC) words and AzBio sentences in quiet and +10 dB signal-to-noise ratio (S/N).

Results

CI1 performance scores at ≥12 months were independently associated with CI2 performance scores at ≥12 months for CNC words (β = 0.371 [0.136–0.606], p = 0.003), AzBio sentences in quiet (β = 0.614 [0.429–0.80], p < 0.0001), and AzBio +10 dB S/N (β = 0.712 [0.459–0.964], p < 0.0001). CI1 scores on AzBio in quiet at 0 to 6 months were also independently associated with CI2 AzBio in quiet scores at ≥12 months (β = 0.389 [0.004–0.774], p = 0.048). Hearing loss etiology and duration, age at implantation, interval between CI1 and CI2, duration of hearing aid use, and preimplantation speech recognition testing scores were not consistently associated with CI2 scores at ≥12 months.

Conclusions

CI1 performance is an independent predictor of second-side performance as measured ≥12 months postimplantation. This may be a clinically useful metric when considering adult sequential bilateral implantation.
Does Compliance or Cost Regulate Effectiveness of Notched Sound Therapy Phone Applications for Tinnitus Relief? Preliminary Data of a Prospective Randomized Control Trial
Authors: Adamovich-Zeitlin Richard , Pelosi Stanley , Mullooly Virginia , Svrakic Maja
Published: January 2023

Objective

The objective of this study is to evaluate compliance with and effectiveness of notched sound therapy (NST) administered through a mobile application in improving symptoms of patients experiencing chronic tinnitus.

Study Design

A prospective randomized control trial was done.

Setting

The study was done at a tertiary referral center.

Patients

Adult patients with tinnitus were monitored.

Interventions

Patients were randomized at enrollment to either the NST or a standard of care (SOC) group. NST arm included, in addition to SOC, a free subscription to NST mobile application, whereas the SOC arm included NST at subscription cost.

Main Outcome Measures

The main outcome measures were continued enrollment in study, compliance with the therapy, frequency and duration of therapy use, and change from the baseline in the Tinnitus Handicap Inventory (THI).

Results

Patients in the NST group were 2.25 times more likely to use the NST application for 3 months postenrollment. Only 33% of users in the NST group listened for the prescribed 2 h/d compared with 0% of users in the SOC group. There was a clinically relevant mean decrease in THI from a baseline of 13.5 in the NST group (p = 0.09) and of 14.8 in the SOC group (p = 0.02). There was a positive correlation between initial THI and decrease in THI after 3 months (p = 0.001).

Conclusions

Monitoring tinnitus for 3 months leads to a decrease in subjective symptoms regardless of NST use. Patients who received a free subscription to the application were more likely to continue with therapy, but very few patients were able to comply with 2 hours of listening time per day.
Reinventing Nuclear Histo-score Utilizing Inherent Morphologic Cutoffs: Blue-brown Color H-score (BBC-HS)
Authors: Price Phillipe , Ganugapati Usharani , Gatalica Zoran , Kakadekar Archan , Macpherson James , Quenneville Louise , Rees Henrike , Slodkowska Elzbieta , Suresh Janarthanee , Yu Darryl , Lim Hyun J. , Torlakovic Emina E.
Published: January 2023

Immunohistochemistry (IHC) is a testing methodology that is widely used for large number of diagnostic, prognostic, and predictive biomarkers. Although IHC is a qualitative methodology, in addition to threshold-based stratification (positive vs. negative), the increasing levels of expression of some of these biomarkers often lead to more intense staining, which published evidence linked to specific diagnosis, prognosis, and responses to therapy. It is essential that the descriptive thresholds between positive and negative staining, as well as between frequently used graded categories of staining intensity (eg, 1+, 2+, 3+) are standardized and reproducible. Histo-score (H-score) is a frequently used scoring system that utilizes these categories. Our study introduces categorization of the cutoff points between positive and negative results and graded categories of staining intensity for nuclear IHC biomarker assays based on color interaction between hematoxylin and diaminobenzidine (DAB); the Blue-brown Color H-score (BBC-HS).

Six cases of diffuse large B-cell lymphoma were stained for a nuclear marker MUM1. The staining was assessed by H-score by 12 readers. Short tutorial and illustrated instructions were provided to readers. The novel scoring system in this study uses the interaction between DAB (DAB, brown stain) and hematoxylin (blue counterstain) to set thresholds between “0” (negative nuclei), “1+” (weakly positive nuclei), “2+” (moderately positive nuclei), and “3+” (strongly positive nuclei). The readers recorded scores for 300 cells. Krippendorff alpha (K-alpha) and intraclass correlation coefficient (ICC) were calculated. We have also assessed if reliability improved when counting the first 100 cells, first 200 cells, and for the total 300 cells using K-alpha and ICC. To assess the performance of each individual reader, the mean H-score and percent positive score (PPS) for each case was calculated, and the bias was calculated between each reader’s score and the mean.

K-alpha was 0.86 for H-score and 0.76 for PPS. ICC was 0.96 for H-score and 0.92 for PPS. The biases for H-score ranged from −58 to 41, whereas for PPS it ranged from −27% to 33%. Overall, most readers showed very low bias. Two readers were consistently underscoring and 2 were consistently overscoring compared with the mean. For nuclear IHC biomarker assays, our newly proposed cutoffs provide highly reliable/reproducible results between readers for positive and negative results and graded categories of staining intensity using existing morphologic parameters. BBC-HS is easy to teach and is applicable to both human eye and image analysis. BBC-HS application should facilitate the development of new reliable/reproducible scoring schemes for IHC biomarkers.
Early angiogenesis dependent CXCL12 attracts Adipose-derived stem cells to promote the repair of fat grafting in a mice model
Authors: Chen Yunzi , Wang Zijue , Li Ye , Li Bin , Wang Xinhui , Zou Jialiang , Bi Xin , Zhao Jing , Lu Feng , Dong Ziqing
Published: January 2023

Background:

The unpredictable and unstable tissue retention rate of autologous fat grafting remains an obstacle faced by plastic surgeons. Our previous study using fat grafting mice model with donor site showed ASCs infiltration in recipient site was delayed, leading to poor regeneration and lower retention. Thus, the mechanism behind the differential infiltration of ASCs required to be explored.

Methods:

Firstly, we locally injected CXCL12 or CXCR4 inhibitor AMD3100 in recipient or donor site respectively (CXCL12+AMD3100-Group, CXCL12-AMD3100+Group, and CXCL12+AMD3100+Group). We compared the migration of ASCs, adipose regeneration and long-term retention. Next, we explored the role of angiogenesis using a Normal/Ischemic mice model in which we test the expression of CXCL12/CXCR4, migration of ASCs, and adipose regeneration.

Results:

Blocking CXCL12 in donor site using AMD3100 (CXCL12-AMD3100+, and CXCL12+AMD3100+Group) could accelerate ASCs infiltration, promote adipose regeneration and long-term retention (p<0.05) compared with the other groups. CXCL12 and its receptor CXCR4 expressed higher in Normal than in Ischemic adipose tissue; consistently, there were more ASCs infiltrating Normal than Ischemic adipose tissue early after surgery (p<0.05).

Conclusion:

Early angiogenesis is essential for CXCL12 in promoting ASCs infiltration, improving adipose tissue repair in recipient site and potentiating long-term fat retention rate.
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
Authors: Sanderson Nicholas D. , Kapel Natalia , Rodger Gillian , Webster Hermione , Lipworth Samuel , Street Teresa L. , Peto Timothy , Crook Derrick , Stoesser Nicole
Published: January 2023

Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short-read (Illumina) datasets. Being able to use nanopore-only data would be a significant advance. Oxford Nanopore Technologies (ONT) have recently released a new flowcell (R10.4) and chemistry (Kit12), which reportedly generate per-read accuracies rivalling those of Illumina data. To evaluate this, we sequenced DNA extracts from four commonly studied bacterial pathogens, namely

Escherichia coli

,

Klebsiella pneumoniae

,

Pseudomonas aeruginosa

and

Staphylococcus aureus

, using Illumina and ONT’s R9.4.1/Kit10, R10.3/Kit12, R10.4/Kit12 flowcells/chemistries. We compared raw read accuracy and assembly accuracy for each modality, considering the impact of different nanopore basecalling models, commonly used assemblers, sequencing depth, and the use of duplex versus simplex reads. ‘Super accuracy’ (sup) basecalled R10.4 reads - in particular duplex reads - have high per-read accuracies and could be used to robustly reconstruct bacterial genomes without the use of Illumina data. However, the per-run yield of duplex reads generated in our hands with standard sequencing protocols was low (typically <10 %), with substantial implications for cost and throughput if relying on nanopore data only to enable bacterial genome reconstruction. In addition, recovery of small plasmids with the best-performing long-read assembler (Flye) was inconsistent. R10.4/Kit12 combined with sup basecalling holds promise as a singular sequencing technology in the reconstruction of commonly studied bacterial genomes, but hybrid assembly (Illumina+R9.4.1 hac) currently remains the highest throughput, most robust, and cost-effective approach to fully reconstruct these bacterial genomes.
Parasitic manipulation or side effects? The effects of pastToxoplasmaandBorreliainfections on human personality and cognitive performance are not mediated by impaired health
Authors: Flegr Jaroslav , Hlaváčová Jana , Toman Jan
Published: January 2023

BacteriaBorrelia burgdorferi s. l. and even more the protozoanToxoplasma gondiiare known to affect the behavior of their animal and human hosts. Both pathogens infect a significant fraction of human population, and both survive in the host’s body for a long time. The resulting latent infections used to be considered clinically asymptomatic. In the last decade, however, numerous studies have shown that this view may be wrong and both infections can have various adverse effects on human health. Their specific behavioral effects may thus be merely side effects of the general impairment of patients’ health. We tested this hypothesis on a cohort of 7,762 members of internet population using a two-hour-long survey consisting of a panel of questionnaires and performance tests. Our findings confirmed that subjects infected withToxoplasmawere in worse physical and mental health and those infected withBorreliawere in worse physical health than corresponding controls. The infected and noninfected subjects also differed in several personality traits (conscientiousness, pathogen disgust, injury disgust, Machiavellianism, narcissism, tribalism, anti-authoritarianism, intelligence, reaction time, and precision). Majority of the behavioral effects associated withBorreliainfection were the same as those associated withToxoplasmainfection, but some dramatically differed (e.g., performance in the Stroop test). Path analyses and nonparametric partial Kendall correlation tests showed that these effects were not mediated by impaired health of the infected individuals. The results thus contradict predictions of the side effects hypothesis.
The ER folding sensor UGGT1 acts on TAPBPR-chaperoned peptide-free MHC I
Authors: Sagert Lina , Winter Christian , Ruppert Ina , Zehetmaier Maximilian , Thomas Christoph , Tampé Robert
Published: January 2023

Adaptive immune responses are triggered by antigenic peptides presented on major histocompatibility complex class I (MHC I) at the surface of pathogen-infected or cancerous cells. Formation of stable peptide-MHC I complexes is facilitated by tapasin and TAPBPR, two related MHC I-specific chaperones that catalyze selective loading of suitable peptides onto MHC I in a process called peptide editing or proofreading. On their journey to the cell surface, MHC I complexes must pass a quality control step performed by UGGT1, which senses the folding status of the transiting N-linked glycoproteins in the endoplasmic reticulum (ER). UGGT1 reglucosylates non-native glycoproteins and thereby allows them to revisit the ER folding machinery. Here, we describe a reconstitutedin-vitrosystem of purified human proteins that enabled us to delineate the function of TAPBPR during the UGGT1-catalyzed quality control and reglucosylation of MHC I. By combining glycoengineering with liquid chromatography-mass spectrometry, we show that TAPBPR promotes reglucosylation of peptide-free MHC I by UGGT1. Thus, UGGT1 cooperates with TAPBPR in fulfilling a crucial function in the quality control mechanisms of antigen processing and presentation.
Bipolar anodal septal pacing with direct LBB capture preserves physiological ventricular activation better than unipolar left bundle branch pacing
Authors: Curila Karol , Jurak Pavel , Prinzen Frits , Jastrzebski Marek , Waldauf Petr , Halamek Josef , Tothova Marketa , Znojilova Lucie , Smisek Radovan , Kach Jakub , Poviser Lukas , Linkova Hana , Plesinger Filip , Moskal Pawel , Viscor Ivo , Vondra Vlastimil , Leinveber Pavel , Osmancik Pavel
Published: January 2023

Background

Left bundle branch pacing (LBBP) produces delayed, unphysiological activation of the right ventricle. Using ultra-high-frequency electrocardiography (UHF-ECG), we explored how bipolar anodal septal pacing with direct LBB capture (aLBBP) affects the resultant ventricular depolarization pattern.

Methods

In patients with bradycardia, His bundle pacing (HBP), unipolar nonselective LBBP (nsLBBP), aLBBP, and right ventricular septal pacing (RVSP) were performed. Timing of local ventricular activation, in leads V1-V8, was displayed using UHF-ECG, and electrical dyssynchrony (e-DYS) was calculated as the difference between the first and last activation. Durations of local depolarizations were determined as the width of the UHF-QRS complex at 50% of its amplitude.

Results

aLBBP was feasible in 63 of 75 consecutive patients with successful nsLBBP. aLBBP significantly improved interventricular dyssynchrony (−9 ms (−12;−6) vs. −24 ms (−27;−21),), p < 0.001) and shortened local depolarization durations in V1–V4 (mean differences −7 ms to −5 ms (−11;−1), p < 0.05) compared to nsLBBP. Both aLBBP and HBP caused similar absolute levels of interventricular dyssynchrony (e-DYS −9 ms (−12; −6) vs. 10 ms (7;14); however, local depolarization durations in V1–V2 during aLBBP were longer than HBP (differences 5–9 ms (1;14), p < 0.05, with local depolarization duration in V1 during aLBBP being the same as during RVSP (difference 2 ms (−2;6), p = 0.52).

Conclusion

Although aLBBP significantly improved interventricular synchrony and depolarization duration of the septum and RV compared to unipolar nsLBBP, the resultant ventricular depolarization was still less physiological than during HBP.
Analysis of recurrent research pathways for assessing and improving effectiveness in life sciences laboratories
Authors: Balas E. Andrew , Patel Charmi , Ewing Ben , Patel Nauka , Curry Tiana , Wise Scott , Abdelgawad Yara H
Published: January 2023

Background

Life sciences research often turns out to be ineffective. Our aim was to develop a method for mapping repetitive research processes, detecting practice variations, and exploring inefficiencies.

Methods

Three samples of R&I projects were used: companion diagnostics of cancer treatments, identification of COVID-19 variants, and COVID-19 vaccine development. Major steps involved: defined starting points, desired end points; measurement of transition times and success rates; exploration of variations, and recommendations for improved efficiency.

Results

Over 50% of CDX developments failed to reach market simultaneously with new drugs. There were significant variations among phases of co-development (Bartlett test P<0.001). Length of time in vaccine development also shows variations (P<0.0001). Similarly, subject participation indicates unexplained variations in trials (Phase I: 489.7 (±461.8); Phase II: 857.3 (±450.1); Phase III: 35402 (±18079).

Conclusion

Analysis of repetitive research processes can highlight inefficiencies and show ways to improve quality and productivity in life sciences.
Neutrophil extracellular trap stabilization by platelet factor 4 reduces thrombogenicity and endothelial cell injury
Authors: Ngo Anh T. P. , Sarkar Amrita , Yarovoi Irene , Levine Nate D. , Bochenek Veronica , Zhao Guohua , Rauova Lubica , Kowalska M. Anna , Eckart Kaitlyn , Mangalmurti Nilam S. , Rux Ann , Cines Douglas B. , Poncz Mortimer , Gollomp Kandace
Published: January 2023

Neutrophil extracellular traps (NETs) are abundant in sepsis, and proposed NET-directed therapies in sepsis prevent their formation or accelerate degradation. Yet NETs are important for microbial entrapment, as NET digestion liberates pathogens and NET degradation products (NDPs) that deleteriously promote thrombosis and endothelial cell injury. We proposed an alternative strategy of NET-stabilization with the chemokine, platelet factor 4 (PF4, CXCL4), which we have shown enhances NET-mediated microbial entrapment. We now show that NET compaction by PF4 reduces their thrombogenicity. In vitro, we quantified plasma thrombin and fibrin generation by intact or degraded NETs and cell-free (cf) DNA fragments, and found that digested NETs and short DNA fragments were more thrombogenic than intact NETs and high molecular weight genomic DNA, respectively. PF4 reduced the thrombogenicity of digested NETs and DNA by interfering, in part, with contact pathway activation. In endothelial cell culture studies, short DNA fragments promoted von Willebrand factor release and tissue factor expression via a toll-like receptor 9-dependent mechanism. PF4 blocked these effects.Cxcl4-/-mice infused with cfDNA exhibited higher plasma thrombin anti-thrombin (TAT) levels compared to wild-type controls. Following challenge with bacterial lipopolysaccharide,Cxcl4-/-mice had similar elevations in plasma TAT and cfDNA, effects prevented by PF4 infusion. Thus, NET-stabilization by PF4 prevents the release of short fragments of cfDNA, limiting the activation of the contact coagulation pathway and reducing endothelial injury. These results support our hypothesis that NET-stabilization reduces pathologic sequelae in sepsis, an observation of potential clinical benefit.

HIGHLIGHTS

In contrast to intact NETs, degraded NETs and cfDNA are prothrombotic and injure the endothelium.

PF4 reduces the ability of degraded NETs and cfDNA to promote thrombosis and injure the endothelium.
Low Rate Hippocampal Delay Period Activity Encodes Behavioral Experience
Authors: Athanasiadis Markos , Masserini Stefano , Yuan Li , Fetterhoff Dustin , Leutgeb Jill K , Leutgeb Stefan , Leibold Christian
Published: January 2023

Remembering what just happened is a crucial prerequisite to form long-term memories but also for establishing and maintaining working memory. So far there is no general agreement about cortical mechanisms that support short-term memory. Using a classifier-based decoding approach, we report that hippocampal activity during few sparsely distributed brief time intervals contains information about the previous sensory motor experience of rodents. These intervals are characterized by only a small increase of firing rate of only a few neurons. These low-rate predictive patterns are present in both working memory and non-working memory tasks, in two rodent species, rats and Mongolian gerbils, are strongly reduced for rats with medial entorhinal cortex lesions, and depend on the familiarity of the sensory-motor context.
Statin-mediated reduction in mitochondrial cholesterol primes an anti-inflammatory response in macrophages by upregulating Jmjd3
Authors: Salloum Zeina , Dauner Kristin , Li Yun-fang , Verma Neha , Zhang John D. , Nakka Kiran , Chen Mei Xi , Valdivieso-González David , Almendro-Vedia Víctor , McDonald Jeffery , Corley Chase D. , Sorisky Alexander , Song Bao-Liang , López-Montero Iván , Luo Jie , Dilworth Jeffrey F. , Zha Xiaohui
Published: January 2023

Stains are known to be anti-inflammatory, but the mechanism remains poorly understood. Here we show that macrophages, either treated with statinin vitroor from statin-treated mice, have reduced cholesterol levels and higher expression ofJmjd3,a H3K27me3 demethylase. We provide evidence that lowering cholesterol levels in macrophages suppresses the ATP synthase in the inner mitochondrial membrane (IMM) and changes the proton gradient in the mitochondria. This activates NFκB andJmjd3expression to remove the repressive marker H3K27me3. Accordingly, the epigenome is altered by the cholesterol reduction. When subsequently challenged by the inflammatory stimulus LPS (M1), both macrophages treated with statinsin vitroor isolated from statin-treated micein vivo, express lower levels pro-inflammatory cytokines than controls, while augmenting anti-inflammatoryIl10expression. On the other hand, when macrophages are alternatively activated by IL4 (M2), statins promote the expression ofArg1,Ym1, andMrc1. The enhanced expression is correlated with the statin-induced removal of H3K27me3 from these genes prior to activation. In addition,Jmjd3and its demethylase activity are necessary for cholesterol to modulate both M1 and M2 activation. We conclude that upregulation ofJmjd3is a key event for the anti-inflammatory function of statins on macrophages.