bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum
Authors: McElroy Kyle E , Audino Jorge A , Serb Jeanne M 
Published: November 2023

Abstract
In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.
Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo
Authors: Zhang Han , Kelly Karen , Lee Jonathan , Echeverria Dimas , Cooper David , Panwala Rebecca , Amrani Nadia , Chen Zexiang , Gaston Nicholas , Wagh Atish , Newby Gregory A , Xie Jun , Liu David R , Gao Guangping , Wolfe Scot A , Khvorova Anastasia , Watts Jonathan K , Sontheimer Erik J 
Published: November 2023

Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a ‘protecting oligo’), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
A Community Social Work Paradigm: Thoughts and Reflections
Authors: Weiss-Dagan Shlomit , Aviv Inbal , Eliyahou Ayala , Levy Drorit , Makaros Ayelet , Freiberg Smadar , Zriker Amit 
Published: November 2023

AbstractCommunity social work (CSW) is often regarded as a practice with a variety of intervention models. The objectives of the present article are to examine CSW’s philosophical and theoretical roots and to bridge the gap in the literature regarding the theoretical and philosophical origins of CSW and to conceptualize these theoretical bases as a paradigm with ontological, epistemological, axiological, and methodological aspects. The ontology of the proposed CSW paradigm relies on ecological theory, critical theory, and community psychology. The paradigm’s epistemology relies on the basic assumption that community members are autonomous subjective human beings with important and valid knowledge who make decisions concerning their lives. Axiologically, the most prominent value of the paradigm is participation, from which other central values derive. The paradigm’s methodology derives from its three abovementioned components. The conceptualization of a CSW paradigm provides a theoretical foundation for community interventions and refining the goals of these interventions. The paradigm can be used as a pedagogical and identity-building tool with students and social workers who focus on CSW.
Meniscus Tear Requiring Intra-Operative Repair Does Not Influence Mid-term Patient Reported Outcomes in Operatively Treated Tibial Plateau Fractures
Authors: Sato Eleanor H. , O’Neill Dillon C. , Steffenson Lillia N. , Myhre Luke A. , Higgins Thomas F. , Rothberg David L. , Marchand Lucas S. , Haller Justin M. 
Published: November 2023

OBJECTIVE:
Evaluate whether intra-operatively repaired lateral meniscus injuries impact mid-term patient reported outcomes in those undergoing operative fixation of tibial plateau fracture.

METHODS:

Design:
Retrospective cohort study.

Setting:
Level I trauma center.

Patient Selection Criteria:
All patients (n=207) who underwent operative fixation of a tibial plateau fracture from 2016-2021 with minimum 10-month follow-up.

Outcome Measures and Comparisons
: The Patient-Reported Outcomes Measurement Information System Physical Function (PROMIS-PF), Knee Injury and Osteoarthritis Outcome Score (KOOS), and the PROMIS-Preference (PROPr) health utility score.

RESULTS:
Overall, 207 patients were included with average follow-up of 2.9 years. Seventy-three (35%) patients underwent intraoperative lateral meniscus repair. Gender, age, body mass index, Charlson Comorbidity Index, days to surgery, ligamentous knee injury, open fracture, vascular injury, polytraumatic injuries, Schatzker classification, and OTA classification were not associated with meniscal repair (p>0.05). Rates of re-operation (42% vs 31%, p=0.11), infection (8% vs 10%, p=0.60), return-to-work (78% vs 75%, p=0.73), and subsequent total knee arthroplasty (8% vs 5%, p=0.39) were also similar between those who had a meniscal repair and those without a meniscal injury, respectively. There was no difference in PROMIS-PF (46.3 vs 45.8, p=0.707), PROMIS-Preference (PROPr) (0.51 vs 0.50, p=0.729), and all KOOS domain scores at final follow-up between those who had a meniscal repair and those without a meniscal injury, respectively.

CONCLUSION:
In patients with an operatively treated tibial plateau fracture, the presence of a concomitant intraoperatively identified and repaired lateral meniscal tear results in similar mid-term PROMs and complication rates when compared to patients without meniscal injury.
Comparison of Fixation Methods between Transosseous Pull-Out Suture and Separate Vertical Wiring for Inferior Pole Fracture of Patella: A Systematic Review and Meta-Analysis
Authors: Kim Kang-Il , Kim Jun-Ho , Son Gwankyu 
Published: November 2023

ABSTRACTObjectives:To compare, in a systematic review, Krakow transosseous (KT) suturing and separate vertical wiring (VW) fixation methods in inferior pole fractures of the patella and to evaluate whether the supplementary fixation affected bone union.Data Sources:The MEDLINE, Embase, and Cochrane databases were searched from inception to January 15, 2023. The keywords were “patella inferior pole fracture”, “patella distal pole fracture”, “transosseous”, “pull-out suture”, “reattachment”, and “vertical wiring”.Study Selection:All clinical studies describing KT or VW techniques for inferior pole fracture of the patella and reporting bone union-related complications were included.Data Extraction:This meta-analysis included 16 studies with 274 patellae. Demographic data, surgical techniques, clinical outcomes, and complication rates were recorded. The Methodological Index for Non-Randomized Studies criteria were used to assess their quality.Data Synthesis:A meta-analysis was performed using random-effects models and meta-regression. The meta-analytic estimate of bone union-related complications was 3.8% (95% CI, 1.6%-6.0%) for either PO or VW techniques in inferior pole fractures of the patella. The bone union-related complication rates did not differ significantly between the two techniques (KT, 5.7%; VW, 3.0%;P=.277). Meanwhile, supplementation fixation was significantly associated with decrease in bone union-related complication rates (p=.013).Conclusion:Fixation of inferior pole fractures of the patella using either KT or VW techniques provided satisfactory and similar clinical results with minimal bone union-related complications. Supplementary fixation has a positive impact on reducing bone union-related complications in inferior pole fractures of the patella following KT and VW techniques.
Three-Dimensional Mapping of Scapular Body, Neck and Glenoid Fractures
Authors: Cole Peter A. , Schroder Lisa K. , Brahme Indraneel S. , Thomas Claire N. , Kuhn Lorenz , Zaehringer Erich , Petersik Andreas 
Published: November 2023

Objectives:
The purpose of this study was to report patterns of scapular fractures and define them with a contemporary methodology.

Methods:

Design:
Retrospective study, 2015 – 2021

Setting:
Single, Academic, Level 1 Trauma Center

Patient Selection Criteria:
Consecutive patients ≥ 18 years, presenting with unilateral scapula fracture, with thin-slice (≤ 0.5 mm) bilateral CT scans of the entirety of both the injured and uninjured scapulae
Outcome Measures and Comparisons:
Thin-slice (0.5 mm) computed tomography (CT) scans of injured and normal scapulae were obtained to create three-dimensional (3D) virtual models. 3D modeling software (Stryker Orthopedics Modeling and Analytics, Stryker Trauma GmbH, Kiel, Germany aka SOMA) was used to create a 3D map of fracture location and frequency. Fracture zones were delineated using anatomic landmarks to characterize fracture patterns.

Results:
87 patients were identified with 75 (86%) extra-articular and 12 (14%) intra-articular fractures. The dominant fracture pattern emanated from the superior lateral border (Zone E) to an area inferior to the spinomedial angle (Zone B) and was present in 80% of extra-articular fractures. A second-most common fracture line propagated from the Primary (most-common) Line towards the inferior medial scapular border with a frequency of 36%. Bare zones (with one or no fractures present) were identified in four unique areas. Furthermore, intra-articular fractures were found to be heterogenous.

Conclusions:
The 3D fracture map created in this study confirmed that extra-articular scapular fractures occur in certain patterns with a relatively high frequency. Results provide greater insight into scapular fracture locations and may help to study prognosis of injury and improve treatment strategy including operative approaches and surgical tactics.
Pde5 Inhibition Reduced Blood Pressure and Alleviated Target Organ Damage in Chronic Intermittent Hypoxia
Authors: Li Siyi , Xin Qingjie , Yan Yan , Wang Xiao , Ai Hui , Que Bin , Gong Wei , Nie Shaoping 
Published: November 2023

Abstract:
The role of phosphodiesterase 5 (Pde5) in obstructive sleep apnea–induced damage remains unclear. Our study aimed to investigate the role of Pde5 in the chronic intermittent hypoxia (CIH) model. C57BL/6J wild-type (WT) mice (n = 48) and Pde5 knockout (Pde5−/−) mice (n = 24) were randomly assigned to CIH group and room air group. After 6 weeks, some WT mice (n = 24) in CIH group were given sildenafil or saline gavage for another 4 weeks. Blood pressure was regularly measured during the experiment. Echocardiography was used to estimate cardiac function. We collected organs from each group of mice and measured their physical indicators. Histochemical staining was used to explore the size of cardiomyocyte and fibrosis area of various organs. Cyclic guanosine monophosphate and malondialdehyde concentrations in serum were measured by ELISA assay. Compared with the RA-treated group, the 6-week CIH resulted in a significant increase in blood pressure, altered heart structure, and reduced serum cyclic guanosine monophosphate in WT mice. Pde5−/− mice and sildenafil intragastric administration significantly reduced systolic blood pressure in CIH condition and attenuated the damage of target organs. In CIH model, we found that the cardiomyocyte size and fibrosis area of heart and kidney significantly reduced in Pde5−/− groups. Besides, endogenous and exogenous inhibition of Pde5 reduced malondialdehyde level and inflammatory and oxidative stress markers expression in CIH condition. In this study, we found that Pde5 inhibition could reduce blood pressure and alleviate target organ damage in the CIH model, which may be mediated through the oxidative stress pathway.
Pushing the limits of treatment for hepatocellular carcinoma
Authors: Jones-Pauley Michelle , Victor David W. , Kodali Sudha 
Published: November 2023

Purpose of review
We review existing and newer strategies for treatment and surveillance of hepatocellular carcinoma (HCC) both pre and postliver transplantation.

Summary
HCC is rising in incidence and patients are often diagnosed at later stages. Consequently, there is a need for treatment strategies which include collaboration of multiple specialties. Combinations of locoregional, systemic, and surgical therapies are yielding better postliver transplantation (post-LT) outcomes for patients with HCC than previously seen. Tumor biology (tumor size, number, location, serum markers, response to therapy) can help identify patients who are at high risk for HCC recurrence posttransplantation and may expand transplant eligibility for some patients.
A narrative review on spontaneous clearance of urogenital Chlamydia trachomatis: Host, microbiome, and pathogen-related factors
Authors: Klasner Carson , Macintyre Andrew N. , Brown Sarah E. , Bavoil Patrik , Ghanem Khalil G. , Nylander Elisabeth , Ravel Jacques , Tuddenham Susan , Brotman Rebecca M. 
Published: November 2023

ABSTRACT

Chlamydia trachomatis (CT) is the most commonly reported sexually transmitted infection in the United States. Untreated urogenital infection in women can result in adverse sequelae such as pelvic inflammatory disease and infertility. Despite national screening and treatment guidelines, rates continue to rise; since most infections are asymptomatic, the actual prevalence of CT infection is likely significantly higher than reported. Spontaneous clearance of CT in women (in the absence of antibiotic treatment) has been described in multiple epidemiologic studies. Given the serious consequences and high prevalence of CT infection, there is growing interest in understanding this phenomenon and factors which may promote CT clearance in women. Spontaneous CT clearance is likely the result of complex interactions between CT, the host immune system, and the vaginal microbiota (i.e., the communities of bacteria inhabiting the vagina) which has been implicated in CT acquisition. Herein, we briefly review current literature regarding the role of each of these factors in spontaneous CT clearance, identify knowledge gaps, and discuss future directions and possible implications for the development of novel interventions which may protect against CT infection, facilitate clearance, and prevent reproductive sequelae.
NUDC is critical for rod photoreceptor function, maintenance, and survival
Authors: Garner Mary Anne , Hubbard Meredith G. , Boitet Evan R. , Hubbard Seth T. , Gade Anushree , Ying Guoxin , Jones Bryan W. , Baehr Wolfgang , Gross Alecia K. 
Published: November 2023

AbstractNUDC (nucleardistribution protein C) is a mitotic protein involved in nuclear migration and cytokinesis across species. Considered a cytoplasmic dynein (henceforth dynein) cofactor, NUDC was shown to associate with the dynein motor complex during neuronal migration. NUDC is also expressed in postmitotic vertebrate rod photoreceptors where its function is unknown. Here, we examined the role of NUDC in postmitotic rod photoreceptors by studying the consequences of a conditional NUDC knockout in mouse rods (rNudC−/−). Loss of NUDC in rods led to complete photoreceptor cell death at six weeks of age. By 3 weeks of age, rNudC-/-function was diminished, and rhodopsin and mitochondria were mislocalized, consistent with dynein inhibition. Levels of outer segment proteins were reduced, but LIS1 (lissencephaly protein 1), a well-characterized dynein cofactor, was unaffected. Transmission electron microscopy revealed ultrastructural defects within the rods of rNudC−/−by 3 weeks of age. We investigated whether NUDC interacts with the actin modulator cofilin 1 (CFL1) and found that in rods, CFL1 is localized in close proximity to NUDC. In addition to its potential role in dynein trafficking within rods, loss of NUDC also resulted in increased levels of phosphorylated CFL1 (pCFL1), which would purportedly prevent depolymerization of actin. Absence of NUDC also induced an inflammatory response in Müller glia and microglia across the neural retina by 3 weeks of age. Taken together, our data illustrate the critical role of NUDC in actin cytoskeletal maintenance and dynein-mediated protein trafficking in a postmitotic rod photoreceptor.Significance StatementNuclear distribution protein C (NUDC) has been studied extensively as an essential protein for mitotic cell division. In this study, we discovered its expression and role in the postmitotic rod photoreceptor cell. In the absence of NUDC in mouse rods, we detected functional loss, protein mislocalization, and rapid retinal degeneration consistent with dynein inactivation. In the early phase of retinal degeneration, we observed ultrastructural defects and an upregulation of inflammatory markers suggesting additional, dynein-independent functions of NUDC.
Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity
Authors: Lian Cheng , Zhang Chunyi , Tian Pan , Tan Qilong , Wei Yu , Zhang Qin , Wang Zixian , Zhang Qixiang , Zhong Mengjie , Zhou Li-Quan , Ke Xisong , Zhang Huabing , Zhu Yao , Li Zhenfei , Cheng Jingdong , Wei Gong-Hong 
Published: November 2023

SummaryZMYND11 encodes an epigenetic reader of histone methylation, functioning as a transcriptional corepressor. However, whether and how ZMYND11 contributes to cancer progression and therapy remains unclear. Here we report that ZMYND11 downregulation is prevalent in cancers and profoundly correlates with adverse prostate cancer patient outcomes. Depletion of ZMYND11 promotes tumor cell growth, migration and invasionin vitroas well as tumor formation and metastasisin vivo. Mechanistically, we find that ZMYND11 exhibits tumor suppressive roles through recognizing arginine-194-methylated HNRNPA1 dependent on its MYND domain, thereby squeezing HNRNPA1 in nucleus and inhibiting the formation of stress granules in cytoplasm. Furthermore, ZMYND11 antagonizes HNRNPA1-driven high PKM2/PKM1 ratio and counteracts PKM2-induced aggressive tumor phenotype. Remarkably, ZMYND11 recognition of HNRNPA1 could be disrupted by pharmaceutical inhibition of arginine methyltransferase PRMT5 while ZMYND11 low-expressing tumors are sensitive to the treatment of PRMT5 inhibitors. Collectively, our study unravels a novel and noncanonical function of ZMYND11 as the nonhistone methyl reader and discovers a mechanism for the requirement of arginine-methylation-mediated ZMYND11-HNRNPA1 association to restrict tumor progression and offers cancer therapeutic targets and potential biomarkers.
Simulating growth of TDP-43 cytosolic inclusion bodies in neurons
Authors: Kuznetsov Andrey V. 
Published: November 2023

AbstractThis paper introduces a mathematical model for the growth of transactive response DNA binding protein of 43 kDa (TDP-43) inclusion bodies in neuron soma. The model’s equations enable numerical determination of the concentrations of TDP-43 dimers, monomers, and aggregates. Assuming all aggregates integrate into the inclusion bodies, the model predicts the size of TDP-43 inclusion bodies. An approximate solution to the model equations is derived for the scenario in which protein degradation machinery is dysfunctional, resulting in infinite half-lives for TDP-43 dimers, monomers, and aggregates. This solution, valid for large times, predicts that the inclusion body’s radius increases proportionally to the cube root of time. To the best of the author’s knowledge, this study presents the first attempt to model the relationship between the size of TDP-43 inclusion bodies and time. The sensitivity analysis of the approximate solution indicates that the concentrations of TDP-43 monomers and aggregates, as well as inclusion body radii, are independent of the kinetic constants. While the numerical solution of the full mathematical model continues to work with finite half-lives, the approximate solution becomes invalid for scenarios with physiologically relevant (finite) half-lives of TDP-43 dimers, monomers, and aggregates. In contrast to the situation with infinite half-lives, the numerical solution shows that for various values of kinetic constants, the curves representing concentrations of monomers and aggregates, as well as the curves depicting inclusion body radii, converge to distinct constant values.
Neural responses to social cues in the accessory olfactory bulb are altered by context and experience
Authors: Dwyer Joseph , Weinberg Maxwell , Dickinson Sarah Y. , Bergan Joseph 
Published: November 2023

AbstractSocial interaction enhances evolutionary fitness by enabling efficient communication of physiological information between individuals. Semiochemicals, that convey socially relevant physiological information, are detected by the vomeronasal organ (VNO) which projects directly to the accessory olfactory bulb (AOB). Mitral and tufted (M/T) neurons in the AOB convey this information from the AOB to a network of brain regions particularly devoted to processing social information and affecting social behavior. The dynamics of social behaviors are shaped by both context and experience. However, our understanding of how alterations in behavior, triggered by the same social cues, correlate with moment-to-moment fluctuations in neural activity within social circuits remains limited. Here, we investigate how context and experience alter the sensory-driven activity of AOB M/T neurons using fiberphotometry and find that the context in which a stimulus is presented can be as important for determining the strength of response as the identity of the stimulus itself.