bluuebunny/crossref_metadata_2025 huggingface dataset:
Glaucoma-Related Risk Factors for Endothelial Cell Loss and Graft Failure After Descemet’s Stripping Automated Endothelial Keratoplasty
Authors: Takemori Hayato , Higashide Tomomi , Kobayashi Akira , Yokogawa Hideaki , Sugiyama Kazuhisa
Published: April 2023

Précis:

Previous trabeculectomy and medical or surgical glaucoma treatment after Descemet’s stripping automated endothelial keratoplasty (DSAEK) were significantly associated with endothelial cell loss and graft failure. The pupillary block was a significant risk factor for graft failure.

Purpose:

To evaluate the long-term risk factors associated with postoperative endothelial cell loss and graft failure after DSAEK in Japanese eyes, with special attention to glaucoma.

Patients and Methods:

This retrospective study involved 117 eyes of 110 consecutive patients with bullous keratopathy who had undergone DSAEK. The patients were classified into 4 groups: (1) no glaucoma group (n = 23 eyes), (2) primary angle closure disease group (n = 32 eyes), (3) glaucoma group that had previously undergone trabeculectomy (n = 44 eyes) (glaucoma with bleb), and (4) glaucoma group that had not previously undergone trabeculectomy (n = 18 eyes) (glaucoma without bleb).

Results:

The cumulative 5-year graft survival rate was 82.1%. The cumulative 5-year graft survival rate among the 4 groups is as follows: no glaucoma (73%), primary angle closure disease (100%), glaucoma with bleb (39%), and glaucoma without bleb (80%). Multivariate analysis revealed that additional glaucoma medication and glaucoma surgery after DSAEK were independent risk factors for endothelial cell loss. Conversely, glaucoma with blebs and pupillary block were independent risk factors for graft failure after DSAEK.

Conclusion:

Previous trabeculectomy and medical or surgical glaucoma treatment after DSAEK were significantly associated with endothelial cell loss and graft failure. Pupillary block was a significant risk factor for graft failure.
Proliferative Vitreoretinopathy Following Transscleral Diode Cyclophotocoagulation
Authors: Bai Amelia , Sharma Abhishek , Chiang Mark Y.
Published: April 2023

Précis:

Transscleral diode laser cyclophotocoagulation may trigger the development of proliferative vitreoretinopathy. Our article demonstrates one such case leading to tractional macula-off retinal detachment in a child with aphakic glaucoma.

Purpose:

The purpose of this article is to describe a case of proliferative vitreoretinopathy (PVR) developing subsequent to transscleral diode laser cyclophotocoagulation (cyclodiode) in a pediatric patient with aphakic glaucoma. PVR most commonly occurs following rhegmatogenous retinal detachment repair; however, to the best of our knowledge, it has never been reported to appear after cyclodiode.

Methods:

Retrospective evaluation of case presentation and intraoperative findings.

Results:

A 13-year-old girl with aphakic glaucoma presented 4 months after cyclodiode of the right eye with a retrolental fibrovascular membrane and anterior PVR. The PVR extended posteriorly over the next month, after which the patient developed a tractional macula-off retinal detachment. Pars Plana vitrectomy was performed, confirming dense anterior and posterior PVR. A review of the literature suggests that an inflammatory cascade, similar to that seen in PVR development following rhegmatogenous retinal detachment, may occur from the destruction of the ciliary body by cyclodiode. As a result, fibrous transformation may occur, likely accounting for the cause of PVR development in this case.

Conclusion:

The pathophysiology of PVR development remains unclear. This case demonstrates that PVR may occur following cyclodiode and should be considered during postoperative monitoring after this procedure.
Patient-Centered Outcomes After a Medication Adherence Intervention: a Pilot Study
Authors: Cho Juno , Song Melinda , Niziol Leslie M. , Heisler Michele , Resnicow Ken , Musch David C. , Lee Paul , Darnley-Fisch Deborah , Newman-Casey Paula Anne
Published: April 2023

Précis:

Self-determination theory (SDT) guided behavioral interventions are effective in improving several patient-centered metrics, including glaucoma-related distress. However, whether improvement in patient-centered metrics can drive an improvement in medication-taking behavior remains to be seen.

Objective:

The 7-month Support, Educate, Empower (SEE) personalized glaucoma coaching program was previously shown to improve glaucoma medication adherence by 21 percent points. This study’s goal was to assess the impact of the SEE program on self-determination theory (SDT) metrics and other patient-centered outcome measures.

Participants and Methods:

Glaucoma patients (≥40 y old, taking ≥1 medication) self-reporting poor medication adherence were recruited at the University of Michigan. Eight surveys (with 10 subscales) were completed before and after the 7-month SEE program. Three surveys assessed changes in SDT (Treatment Self-regulation Questionnaire, Healthcare-Climate Questionnaire, Perceived Competence) while the others assessed participants’ Glaucoma Knowledge, Glaucoma Medication Self-efficacy, Glaucoma-related distress, Perceived benefits, confidence asking and getting questions answered.

Results:

Thirty-nine participants completed the SEE program. Significant improvements were in 7 subscales, including all three SDT tenets of competence (mean change =0.9, SD =±1.2, adjusted P=0.0002), autonomy (0.5, ±0.9, 0.044), and relatedness (P=0.002). Glaucoma-related distress (−2.0, ±3.2, 0.004), confidence in asking questions (1.1, ±2.0, 0.008), and confidence in getting questions answered (1.0, ±2.0, 0.009) also improved. Glaucoma-related distress was correlated with perceived competence (r=−0.56, adjusted P=0.005), and an increase in perceived competence was associated with a decrease in glaucoma-related distress (β=−0.43, 95% CI −0.67 - −0.20, adjusted P=0.007).

Conclusions:

The SEE program improved participants’ autonomous motivation, perceived support, perceived competence, glaucoma-related distress, and competence. These results point to the promising potential of SDT-guided behavioral interventions in improving patient-centered metrics.
Pediatric Liver Abscess: Outcomes of Protocol-based Management and Predictors of Poor Outcome
Authors: Anand Mugdha , Sahi Puneet Kaur , Mandal Anirban
Published: April 2023

Background:

Liver abscess (LA) is an important cause of morbidity in children, especially in tropical countries. There is a paucity of data in pediatric LA with no standard guidelines regarding the best modality of treatment and drainage. With a large influx of patients at our center and protocol-based management; we aimed to study clinic-radiologic profile, risk factors, complications and outcomes of children with liver abscess and assessed possible predictors for poor outcomes.

Materials and methods:

This retrospective observational study was conducted from January 2019 to September 2019 at a tertiary care hospital in India. Records of all children (<12 years of age) with ultrasonographically diagnosed liver abscess were accessed for clinic-radiological and demographic profile, laboratory investigations, treatment, complications and outcomes. Patients were categorized into favorable or unfavorable groups based on predefined criteria and were compared for possible predictors of poor outcomes. Outcomes for the protocol-based management were analyzed.

Results:

There were 120 cases of pediatric liver abscess with a median age of 5 years at presentation. The commonest clinical features were fever (100%) and pain in the abdomen (89.16%). The majority of liver abscesses were solitary (78.4%) and in the right lobe (73.3%). Malnutrition was present in 27.5%, overcrowding for 76.5% of patients and worm infestation in 2.5% of patients. Age-related leukocytosis (P = 0.004), neutrophilia (P = 0.013), elevated Aspartate transaminase (P = 0.008), elevated alanine transaminase (P = 0.007) and hypoalbuminemia (P = 0.014) were significantly more in the unfavorable group. Overall, 29.2% of patients underwent conservative management with antibiotics alone, 25.0% underwent percutaneous needle aspiration (PNA), 49.1% underwent ultrasound-guided percutaneous drain (PCD) insertion and open surgical drainage (OSD) was needed in a single patient. The success rate was 100% for conservative management, 76.6% for PNA, 94.7% for PCD and 100% for OSD with an overall mortality of 2.5%.

Conclusions:

Age-related leukocytosis, neutrophilia, elevated aspartate transaminase or alanine transaminase and hypoalbuminemia at presentation are predictors of poor outcomes in pediatric liver abscess. Protocol-based management leads to the appropriate use of PNA and PCD while decreasing mortality and morbidity related to either.
Modern use of tranexamic acid in facial plastic surgery
Authors: Luetzenberg Friederike S. , Lyford-Pike Sofia
Published: April 2023

Purpose of review

Although tranexamic acid is commonly used in surgical fields such as obstetrics, orthopedics, and trauma, its utilization in facial plastic surgery is a recently emerging concept, and studies examining its potential impact have been few. This review highlights how tranexamic acid may be employed during facial plastic procedures and the promising impact it may have.

Recent findings

Tranexamic acid is primarily being studied in rhinoplasties and rhytidectomies, with intravenous administration and local infiltration being the most common routs of application, respectively. During rhinoplasties, tranexamic acid has the potential to improve the visualization of the surgical field by decreasing blood loss and to improve postoperative edema and ecchymosis. For rhytidectomies, on the contrary, it may shorten time to attain hemostasis, lessen the rate of hematoma formation, and lead to lower surgical drain output. Its efficacy is preserved at low doses, and significant medication side effects have not been reported after facial plastic procedures.

Altogether, tranexamic acid may present a valuable adjuvant to facial plastic surgery, as it could increase both surgeon and patient satisfaction while exhibiting a benign safety profile.
The buried guide suture method: a novel technique to correct traumatic facial dimples
Authors: Yuan Ye , Chai Hongli , Wang Lianzhao , Yuan Li , Li Fengyong , Zhou Yu , Cao Yujiao , Liu Meichen , Li Qiang , Li Senkai
Published: April 2023

Facial dimple, frequently following blunt trauma, presents as soft tissue depression, which is particularly apparent during facial expression. The displacement of subcutaneous tissue can be detected and measured by high-frequency ultrasound. Limited surgical methods have been applied in these closed injury cases. It is challenging to reposition the subcutaneous tissue without incisions on unscarred skin. The authors propose a novel three-dimensional technique to suture and fix the subcutaneous tissue at a distance through a concealed incision. The buried guide suture method was used in the treatment of 22 patients suffering from traumatic facial dimples on the cheek. All the patients showed great improvement in their depressed deformity with minor complications. This technique provides an option to correct soft tissue depression without leaving visible scar, especially for the mimetic rupture caused by blunt trauma.

Facial contusions occur frequently in children. Treatments for closed soft tissue injury are easily ignored due to no laceration on the epidermis. However, facial soft tissue depression might appear after the swelling subsides. It usually presents as a dimple that is not conspicuous at rest but exaggerates when patients smile or make other expressions.
Deep circumflex iliac artery flap reconstruction in Brown’s Class I defect of mandible using a three-component surgical template system
Authors: Zheng Chongyang , Xu Xiaofeng , Jiang Tengfei , Zhang Xinyu , Yin Xuelai , Yang Rong , Zhang Zhiyuan , Hu Yongjie
Published: April 2023

Background:

Computer assisted surgery (CAS) is widely used in mandibular reconstruction, but the process is not well-described for cases using deep circumflex iliac artery (DCIA) flap as the donor site. This study aimed to present a DCIA-based three-component surgical template system (3-STS) in patients with mandibular Brown’s Class I defect.

Methods:

This retrospective cohort study compared clinical outcomes of mandibular reconstruction with DCIA flap using 3-STS or conventional surgical templates. The primary outcome of the study was the accuracy of reconstruction, and the secondary outcomes included surgical time and bone flap ischemia time. Surgery-related parameters and functional outcomes were also recorded and compared.

Results:

Forty-four patients (23 in 3-STS; 21 in control group) were included between 2015 and 2021. Compared with the control group, the 3-STS group had higher accuracy of reconstruction, indicated by lower deviation in absolute distance (1.45±0.76 mm vs 2.02±0.89 mm, P=0.034), and less deviation in coronal and sagittal angles (0.86°±0.53° vs 1.27°±0.59°, P=0.039, and 2.52°±1.00° vs 3.25°±1.25°, P=0.047) between pre- and post-operative CT imaging. Surgical time and bone flap ischemia time were significantly reduced in the 3-STS group compared with control group (median time, 385 min vs 445 min and 32 min vs 53 min, respectively; P<0.001). Additionally, masseter attachment was preserved in the 3-STS group but not the control group. No differences were found in adverse events or other clinical variables.

Conclusions:

The 3-STS can improve accuracy, simplify intra-operative procedures to increase surgical efficiency, and preserve functionality in mandibular reconstruction for Brown’s Class I defect.
Functional outcomes and associated factors of individuals with unilateral traumatic lower limb amputation in Sri Lanka: An observational study
Authors: Dasanayaka Dasanayaka Arachchillage Renuka Kusum , Patwary Fazlul Karim , van Ravensberg Clara Dorothea
Published: April 2023

Background:

Rehabilitation is important after an amputation surgery. This study was conducted to find the level of functional outcomes of individuals with unilateral traumatic lower limb amputation and the impact of sociodemographic, amputation, and rehabilitation characteristics on functional outcomes.

Methods:

An observational cross-sectional study was conducted with 48 participants (aged 20–60 years) who visited the Center for Handicapped from across the country. Functional outcomes were measured using the Locomotor Capabilities Index, Amputee Mobility Predictor with Prosthesis, 6-minute walk distance, and spirometry test and sociodemographic, amputation, and rehabilitation characteristics using a self-constructed questionnaire.

Results:

Amputee Mobility Predictor with Prosthesis K levels showed 65% had the ability to ambulate in the community and could master environmental barriers. Locomotor Capabilities Index scores showed 96% could independently perform basic daily activities with or without using assistive devices and 83% could perform advanced daily activities. None of the individuals had achieved their predicted 6-minute walk distance, but 52% had “good and above” level of maximum oxygen consumption; restrictive respiratory pattern was indicated among 31%. Amputee Mobility Predictor with Prosthesis and Locomotor Capabilities Index scores were significantly (p < 0.005) affected by mobility hours/day, amputation level, prosthesis usage, and satisfaction. Six-minute walk distance was significantly (p < 0.005) related to income, time since amputation, duration of rehabilitation, mobility hours/day, sex, job engagement, previous job, amputation level, K levels, and satisfaction with prosthesis.

Conclusion:

Rehabilitation in Sri Lanka mainly focuses on basic walking training, not on long-term survival, distance walking, and cardiorespiratory endurance, which can lead to future comorbidities. Raising awareness in the society about rehabilitation services and more effective rehabilitation programs are recommended.
Anorexia Nervosa With Comorbid Severe Depression
Authors: Andersson Peter , Jamshidi Esmail , Ekman Carl-Johan , Tedroff Kristina , Björkander Jonnie , Sjögren Magnus , Lundberg Johan , Jokinen Jussi , Desai Boström Adrian E.
Published: April 2023

Major depressive disorder (MDD) is highly prevalent in individuals with anorexia nervosa (AN) and is a predictor of greater clinical severity. However, there is a limited amount of evidence supporting the use of psychotropic medications for its management. A systematic scoping review was conducted to assess the current literature on brain stimulation treatments for AN with comorbid MDD, with a specific focus on MDD treatment response and weight restoration. This review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, and the PubMed, PsycInfo, and MEDLINE databases were searched until July 2022 using specific key words related to AN and brain stimulation treatments. A total of 373 citations were identified, and 49 treatment studies that met the inclusion criteria were included in the review. The initial evidence suggests that electroconvulsive therapy, repetitive transcranial magnetic stimulation, and deep-brain stimulation may be effective in managing comorbid MDD in AN. Emerging evidence suggests that transcranial direct current stimulation may have a positive effect on body mass index in individuals with severe to extreme AN. However, there is a need for the development of better measurement techniques for assessing the severity of depression in the context of AN. Controlled trials that are adequately designed to account for these limitations are highly warranted for deep-brain stimulation, electroconvulsive therapy, and repetitive transcranial magnetic stimulation and hold promise for providing clinically meaningful results.
Engineering aphid transmission of foxtail mosaic virus in the presence of potyvirus helper component proteinase through coat protein modifications
Authors: Jiang Jun , Yu Eric , Nihranz Chad T. , Prakash Ved , Varsani Suresh , Casteel Clare L.
Published: April 2023

Biotechnologies that use plant viruses as plant enhancement tools have shown great potential to flexibly engineer crop traits, but field applications of these technologies are still limited by efficient dissemination methods. Potyviruses can be rapidly inoculated into plants by aphid vectors due to the presence of the potyviral helper component proteinase (HC-Pro), which binds to the DAG motif of the coat protein (CP) of the virion. Previously it was determined that a naturally occurring DAG motif in the non-aphid-transmissible potexvirus, potato aucuba mosaic virus (PAMV), is functional when a potyviral HC-Pro is provided to aphids in plants. The DAG motif of PAMV was successfully transferred to the CP of another non-aphid-transmissible potexvirus, potato virus X, to convey aphid transmission capabilities in the presence of HC-Pro. Here, we demonstrate that DAG-containing segments of the CP from two different potyviruses (sugarcane mosaic virus and turnip mosaic virus), and from the previously used potexvirus, PAMV, can make the potexvirus, foxtail mosaic virus (FoMV), aphid-transmissible when fused with the FoMV CP. We show that DAG-containing FoMVs are transmissible by aphids that have prior access to HC-Pro through potyvirus-infected plants or ectopic expression of HC-Pro. The transmission efficiency of the DAG-containing FoMVs varied from less than 10 % to over 70 % depending on the length and composition of the surrounding amino acid sequences of the DAG-containing segment, as well as due to the recipient plant species. Finally, we show that the engineered aphid-transmissible FoMV is still functional as a plant enhancement resource, as endogenous host target genes were silenced in FoMV-infected plants after aphid transmission. These results suggest that aphid transmission could be engineered into non-aphid-transmissible plant enhancement viral resources to facilitate their field applications.
Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
Authors: Pacchiarini Nicole , Cronin Michelle , Sawyer Clare , Williams Catie , Beazer Andrew , Cottrell Simon , Morgan Mari , Saunders Vince , Moore Catherine , Connor Thomas R. , Williams Christopher
Published: April 2023

Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations that may increase transmissibility, severity or vaccine escape. We present a genomic and epidemiological description of a new recombinant lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), XR, first identified in Wales. The Pathogen Genomics Unit (Public Health Wales, UK) sequences positive SARS-CoV-2 PCR tests using the ARTIC SARS-CoV-2 sequencing protocol. Recombinants were detected using an in-house pipeline and the epidemiological data analysed in R. Nosocomial cases were defined as those with samples taken after >7 days in hospital. Between February and March 2022, we identified 78 samples with highly similar genomes, comprising a BA.1-like 5' end, a BA.2-like 3' end and a BA.2-like spike protein. This signature is consistent with recombination and was defined as XR by Pangolin (PANGO v1.8). A total of 50 % of cases had a sample collected whilst in hospital and the first three cases were immunocompromised patients. The patient median age was 58 years (range: 4–95 years) and most of the patients were fully vaccinated against SARS-CoV-2 (74 % third dose/booster). Three patients died within 28 days of their sample collection date, one of whom had COVID-19 listed amongst ICD10 (International Classification of Diseases 10) coded causes of death. Our integrated system enabled real-time monitoring of recombinant SARS-CoV-2 for early detection, in order to rapidly risk assess and respond. This work highlights the importance of setting-based surveillance of recombinant SARS-CoV-2, as well as the need to monitor immunocompromised populations through repeat testing and sequencing.
Performance of ChatGPT, GPT-4, and Google Bard on a Neurosurgery Oral Boards Preparation Question Bank
Authors: Ali Rohaid , Tang Oliver Y. , Connolly Ian D. , Fridley Jared S. , Shin John H. , Zadnik Sullivan Patricia L. , Cielo Deus , Oyelese Adetokunbo A. , Doberstein Curtis E. , Telfeian Albert E. , Gokaslan Ziya L. , Asaad Wael F.
Published: April 2023

Background

General large language models (LLMs), such as ChatGPT (GPT-3.5), have demonstrated capability to pass multiple-choice medical board examinations. However, comparative accuracy of different LLMs and LLM performance on assessments of predominantly higher-order management questions is poorly understood.

Objective

To assess performance of three LLMs (GPT-3.5, GPT-4, and Google Bard) on a question bank designed specifically for neurosurgery oral boards examination preparation.

Methods

The 149-question Self-Assessment Neurosurgery Exam (SANS) Indications Exam was used to query LLM accuracy. Questions were input in a single best answer, multiple-choice format. Chi-squared, Fisher’s exact, and univariable logistic regression tests assessed differences in performance by question characteristics.

Results

On a question bank with predominantly higher-order questions (85.2%), ChatGPT (GPT-3.5) and GPT-4 answered 62.4% (95% confidence interval [CI]: 54.1-70.1%) and 82.6% (95% CI: 75.2-88.1%) of questions correctly, respectively. In contrast, Bard scored 44.2% (66/149, 95% CI: 36.2-52.6%). GPT-3.5 and GPT-4 demonstrated significantly higher scores than Bard (bothP<0.01), and GPT-4 significantly outperformed GPT-3.5 (P=0.023). Among six subspecialties, GPT-4 had significantly higher accuracy in the Spine category relative to GPT-3.5 and in four categories relative to Bard (allP<0.01). Incorporation of higher-order problem solving was associated with lower question accuracy for GPT-3.5 (OR=0.80,P=0.042) and Bard (OR=0.76,P=0.014), but not GPT-4 (OR=0.86,P=0.085). GPT-4’s performance on imaging-related questions surpassed GPT-3.5’s (68.6% vs. 47.1%,P=0.044) and was comparable to Bard’s (68.6% vs. 66.7%,P=1.000). However, GPT-4 demonstrated significantly lower rates of “hallucination” on imaging-related questions than both GPT-3.5 (2.3% vs. 57.1%,P<0.001) and Bard (2.3% vs. 27.3%,P=0.002). Lack of question text description for imaging predicted significantly higher odds of hallucination for GPT-3.5 (OR=1.45,P=0.012) and Bard (OR=2.09,P<0.001).

Conclusion

On a question bank of predominantly higher-order management case scenarios intended for neurosurgery oral boards preparation, GPT-4 achieved a score of 82.6%, outperforming ChatGPT and Google’s Bard.
Transcriptomic and metabolomic characterization of antibacterial activity ofMelastoma dodecandrum
Authors: Poh Wee Han , Ruhazat Nur Syahirah , Yang Lay Kien , Shivhare Devendra , Lim Peng Ken , Kanagasundaram Yoganathan , Rice Scott A. , Mutwil Marek
Published: April 2023

Antibacterial resistance poses a significant global threat, necessitating the discovery of new therapeutic agents. Plants are a valuable source of secondary metabolites with demonstrated anticancer and antibacterial properties. In this study, we reveal that Melastoma dodecandrum exhibits both bacteriostatic and bactericidal effects against Pseudomonas aeruginosa and Staphylococcus aureus. Treatment with plant extracts results in membrane damage and a reduction in Pseudomonas swimming and swarming motility. A comparative analysis of bacterial transcriptomes exposed to Melastoma extracts and four distinct antibiotics indicates that the extracts trigger similar transcriptomic responses as triclosan, a fatty acid inhibitor. Activity-guided fractionation suggests that the antibacterial activity is not attributable to hydrolyzable tannins, but to unidentified minor compounds. Additionally, we identified 104 specialized metabolic pathways and demonstrated a high level of transcriptional coordination between these biosynthetic pathways and phytohormones, highlighting potential regulatory mechanisms in plant metabolism.
Using the SSVEP to measure the SNARC-spatial attention effects in a parity judgment task
Authors: Mora-Cortes A. , Gulbinaite R. , Ridderinkhof K.R. , Cohen M X.
Published: April 2023

Mental representation of numbers in the brain has been described as spatially organized on what is known as the “mental number line,” with small numbers to the left and large numbers to the right. This representation leads to the “SNARC effect” (Spatial-Numerical Association of Response Codes), which refers to (1) improved behavioral performance for “congruent” conditions (e.g., left-handed response to small numbers) as compared to “incongruent” conditions (e.g., right-handed response to small numbers) and (2) perceiving numbers induces an automatic shift in covert spatial attention. Nonetheless, there is scarce physiological evidence for (or against) the prediction that number magnitude induces an automatic shift of spatial attention. Here we recorded EEG during the bimanual SNARC-parity judgment task (classifying numbers as odd or even) in attempt to find electrophysiological evidence for number-magnitude-induced automatic shifts of spatial attention. Attention was measured using the SSVEP (steady-state visual evoked potential) from four task-irrelevant flickering frequencies (two to the left: 15 and 20 Hz and two to the right: 24 and 17.14 Hz) in combination with an optimal spatial filtering method. EEG analysis was performed on the flicker frequencies closest to the fixation point: 20 and 24 Hz for the left and right visual hemifields, respectively. We replicated the expected behavioral patterns predicted by the SNARC effect, such that participants performed better for congruent conditions than on incongruent conditions. We observed significant changes in the SSVEP amplitude with respect to the baseline for the left (20 Hz) and right (24 Hz) flicker for both the congruent and incongruent conditions. Statistically significant differences between the congruent and incongruent conditions were larger for the congruent conditions for the flicker stimuli on the left. Together, these findings support the hypothesis that when numbers are part of the task, but their magnitude is not relevant, the SNARC-spatial attention effect is elicited as a cognitive effect resulting from the mental representation of numbers and its relationship with the space representation, more than merely a motor effect.
PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles
Authors: Aina Adekunle , Hsueh Shawn C.C. , Plotkin Steven S.
Published: April 2023

The comparison of protein conformational ensembles is of central importance in structural biology. However, there are few computational methods for ensemble comparison, and those that are readily available, such as ENCORE, utilize methods that are sufficiently computationally expensive to be prohibitive for large ensembles. Here, a new method is presented for efficient representation and comparison of protein conformational ensembles. The method is based on the representation of a protein ensemble as a vector of probability distribution functions (pdfs), with each pdf representing the distribution of a local structural property such as the number of contacts between Cβatoms. Dissimilarity between two conformational ensembles is quantified by the Jensen Shannon distance between the corresponding set of probability distribution functions. The method is validated for conformational ensembles generated by molecular dynamics simulations of ubiquitin, as well as experimentally derived conformational ensembles of a 130 amino acid truncated form of human tau protein. In the ubiquitin ensemble dataset, the method was up to 88 times faster than the existing ENCORE software, while simultaneously utilizing 48 times fewer computing cores. We make the method available as a Python package, called PROTHON, and provide a GitHub page with the Python source code athttps://github.com/PlotkinLab/Prothon.
New paradigms in actomyosin energy transduction: critical evaluation of non-traditional models for orthophosphate release
Authors: Månsson Alf , Usaj Marko , Moretto Luisa , Matusovsky Oleg , Velayuthan Lok Priya , Friedman Ran , Rassier Dilson E
Published: April 2023

Release of the ATP hydrolysis product inorganic phosphate (Pi) from the active site of myosin is central in chemo-mechanical energy transduction and closely associated with the main force-generating structural change, the power-stroke. Despite intense investigations, the relative timing between Pi-release and the power-stroke remains poorly understood. This hampers in depth understanding of the production of force and motion by myosin in health and disease and also our understanding of myosin-active drugs. From the 1990s and up to today, models with the Pi-release either distinctly before or after the power-stroke, in unbranched kinetic schemes, have dominated the literature. However, in recent years, alternative models have emerged to explain apparently contradictory findings. Here, we first compare and critically analyze, three influential alternative models, either characterized by a branched kinetic scheme or by partial uncoupling of Pi-release and the power-stroke. Finally, we suggest critical tests of the models aiming for a unified picture.
The effects of age on neural correlates of recollection: transient versus sustained fMRI effects
Authors: Hou Mingzhu , de Chastelaine Marianne , Rugg Michael D.
Published: April 2023

Prior fMRI findings in young adults indicate that recollection-sensitive neural regions dissociate according to the time courses of their respective recollection effects. Here, we examined whether such dissociations are also evident in older adults. Young and older participants encoded a series of word-object image pairs, judging which of the denoted objects was the smaller. At test, participants first judged whether a test word was old or new. For items judged old, they were required to recall the associated image and hold it in mind across a variable delay period. A post-delay cue denoted which of three judgments should be made on the retrieved image. Older adults demonstrated significantly lower associative memory performance than young adults. Replicating prior findings, transient recollection effects were identified in the left hippocampus, medial prefrontal cortex and posterior cingulate, while sustained effects were widespread across left lateral cortex and were also evident in the bilateral striatum. With the exception of those in the left insula, all effects were age-invariant. These findings add to the evidence that recollection-related BOLD effects in different neural regions can be temporally dissociated. Additionally, the findings suggest that both transient and sustained recollection effects are largely stable across much of the healthy adult lifespan.
Automated Protein Affinity Optimization using a 1D-CNN Deep Learning Model
Authors: McWhirter J.Liam , Mukhopadhyay Abhishek , Farber Patrick , Lakatos Greg , Dixit Surjit
Published: April 2023

Functional biologics design is a multi-objective optimization problem often with competing design objectives. We report on a novel deep learning based protein sequence prediction framework, ZymeSwapNet, that can be customized to handle a wide range of quantifiable design objectives, a current limitation of traditional protein design methods. We train a simple convolutional neural network (1D-CNN) on nonredundant curated protein crystal structures, using a set of geometric and topological features that describes a local protein environment, to predict the likelihood of each amino acid type for residue sites in the design region. While the model can be directly used to rank templates derived from mutagenesis campaigns, we extend the scope by developing a sequence/mutation generator that optimizes the desired multivariate distribution using a Monte-Carlo sampling. Using a case study – the design of a stable heterodimeric Fc (HetFc) antibody domain – we show that we can further include a Metropolis criterion to bias the sampling to enhance features such as the heterodimeric binding specificity, in addition to original sampling objective of enhancing stability. We demonstrate that ZymeSwapNet can generate stable HetFc designs, within minutes that had taken several rounds of rational structure and physical force-field based modeling attempts.
FGF-21 Conducts a Liver-Brain-Kidney Axis to Promote Renal Cell Carcinoma
Authors: Li Zongyu , Zhang Xinyi , Zhu Wanling , Zhang Cuiling , Sadak Katherine , Halberstam Alexandra A. , Brown Jason R. , Perry Curtis J. , Bunn Azia , Braun David A. , Adeniran Adebowale , Lee Sangwon , Wang Andrew , Perry Rachel J.
Published: April 2023

Metabolic homeostasis is one of the most exquisitely tuned systems in mammalian physiology. Metabolic homeostasis requires multiple redundant systems to cooperate to maintain blood glucose concentrations in a narrow range, despite a multitude of physiological and pathophysiological pressures. Cancer is one of the canonical pathophysiological settings in which metabolism plays a key role. In this study, we utilized REnal Gluconeogenesis Analytical Leads (REGAL), a liquid chromatography-mass spectrometry/mass spectrometry-based stable isotope tracer method that we developed to show that in conditions of metabolic stress, the fasting hepatokine fibroblast growth factor-21 (FGF-21)1, 2coordinates a liver-brain-kidney axis to promote renal gluconeogenesis. FGF-21 promotes renal gluconeogenesis by enhancing β2 adrenergic receptor (Adrb2)-driven, adipose triglyceride lipase (ATGL)-mediated intrarenal lipolysis. Further, we show that this liver-brain-kidney axis promotes gluconeogenesis in the renal parenchyma in mice and humans with renal cell carcinoma (RCC). This increased gluconeogenesis is, in turn, associated with accelerated RCC progression. We identify Adrb2 blockade as a new class of therapy for RCC in mice, with confirmatory data in human patients. In summary, these data reveal a new metabolic function of FGF-21 in driving renal gluconeogenesis, and demonstrate that inhibition of renal gluconeogenesis by FGF-21 antagonism deserves attention as a new therapeutic approach to RCC.
Evolution and Genetic Characterization of Seoul Virus in Wild RatsRattus Norvegicusfrom an urban park in Lyon, France 2020-2022
Authors: Alburkat Hussein , Smura Teemu , Bouilloud Marie , Pradel Julien , Anfray Gwendoline , Berthier Karine , Dutra Lara , Loiseau Anne , Niamsap Thanakorn , Olander Viktor , Sepulveda Diana , Venkat Vinaya , Charbonnel Nathalie , Castel Guillaume , Sironen Tarja
Published: April 2023

Seoul virus (SEOV) is an orthohantavirus primarily carried by rats that can cause hemorrhagic fever with renal syndrome (HFRS) in humans. Nowaday s, its incidence is likely underestimated. We developed a comprehensive serological and molecular characterization of SEOV inRattus norvegicuspopulation from a popular urban park within a large city (‘Park of La Tête d’Or’, Lyon, France) between 2020 and 2022. We confirmed the circulation of SEOV in rats from the park (seroprevalence 17.2%). The SEOV strains detected showed high genetic similar ity with the strain previously described in 2013 in this area. We found low structuring of wild rat populations within Lyon city. This study confirms the circulation of SEOV in Lyon city, in a park where opportunities for SEOV transmission to humans are numerous. Given the high gene flow between rat populations in the park and the rest of the city, we recommend conducting city-wide SEOV surveillance.
Non-specific recognition of histone modifications by H3K9bhb antibody
Authors: Tsusaka Takeshi , Oses-Prieto Juan A. , Lee Christina , DeFelice Brian C. , Burlingame Alma L. , Goldberg Emily
Published: April 2023

Ketone bodies are short chain fatty acids produced in the liver during periods of limited glucose availability that provide an alternative source of energy for the brain, heart, and skeletal muscle. Beyond this classical metabolic role, β-hydroxybutyrate (BHB), is gaining recognition as a pleiotropic signaling molecule. Lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification in which BHB is covalently attached to lysine ε-amino groups. This novel protein adduct is metabolically sensitive, dependent on BHB concentration, and found on proteins in multiple intracellular compartments, including the mitochondria and nucleus. Therefore, Kbhb is hypothesized to be an important component of ketone body-regulated physiology. Kbhb on histones is proposed to be an epigenetic regulator, which links metabolic alterations to gene expression. However, we found that the widely used antibody against the β-hydroxybutyrylated lysine 9 on histone H3 (H3K9bhb) also recognizes other modification(s), which are increased by deacetylation inhibition and include likely acetylations. Therefore, caution must be used when interpreting gene regulation data acquired with the H3K9bhb antibody.
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology
Authors: Hicks Alan , Abraham Paul , Leite Wellington , Zhang Qiu , Weiss Kevin L. , O'Neill Hugh , Petridis Loukas , Smith Jeremy C.
Published: April 2023

The contrast-variation method in small-angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ. By altering the ρ of the target solute and the solvent through judicious incorporation of deuterium, the scattering of desired solute features can be highlighted. Most contrast-variation methods focus on highlighting specific bulk solute elements, but not on how the scattering at specific scattering vectors q, which are associated with specific structural distances, changes with contrast. Indeed, many systems exhibit q-dependent contrast effects. Here, a method is presented for calculating both bulk contrast-match points and q-dependent contrast using 3D models with explicit solute and solvent atoms and SASSENA, an explicit-atom SANS calculator. The method calculates the bulk contrast-match points within 2.4% solvent D2O accuracy for test protein–nucleic acid and lipid nanodisc systems. The method incorporates a general model for the incorporation of deuterium at non-exchangeable sites that was derived by performing mass spectrometry on green fluorescent protein. The method also decomposes the scattering profile into its component parts and identifies structural features that change with contrast. The method is readily applicable to a variety of systems, will expand the understanding of q-dependent contrast matching and will aid in the optimization of next-generation neutron scattering experiments.
Nothing for us, without us: a review of the clinical literature and discursive evidence of interpersonal trauma in autistic women
Authors: Schnabel Alexandra , Bastow Clem
Published: April 2023

Purpose

From the authors’ personal and professional experiences, they have observed that autistic women are uniquely at risk of interpersonal trauma. Given the tendency for autistic women to be overlooked in research and practice, this study aims to rectify this by exploring the relevant literature and including the voices of autistic women throughout this paper.

Design/methodology/approach

This study completed a literature review of quantitative and qualitative data relating to exposure to interpersonal trauma in autistic women. This study also reviewed relevant discursive evidence available on in memoirs and reports. This study also included dialogue between us as authors from an auto/“Autie”-ethnographic position.

Findings

Both clinical literature and discursive evidence support the idea that autistic women are uniquely at risk of interpersonal trauma, in particular, sexual victimisation. Explanatory factors are considered. Studies exploring rates of post-traumatic stress disorder (PTSD) were less consistent. Further evidence is required to better understand how autistic women experience and express PTSD and to inform assessment and treatment modifications.

Originality/value

To the best of the authors’ knowledge, this is the first paper to integrate clinical literature and discursive evidence on the topic of interpersonal trauma in autistic women. It provides useful insights into the experiences of autistic women in this space, directions for urgently needed future research and modifications to clinical practice.
Hearing and being heard: LGBTQIA+ cross-disciplinary collection development
Authors: Pavenick Alexis , Martinez George
Published: April 2023

Purpose

The purpose of this paper is to share how informal cross-disciplinary outreach methods can increase the development, awareness, investment and circulation of lesbian, gay, bisexual, transgender, queer, intersex, asexual (LGBTQIA+) collection in an academic library. The authors believe the methods shown here may be used to develop any collection, as well as increase awareness and use of a collection.

Design/methodology/approach

Through five different low-stakes outreach strategies, the authors connected directly with campus faculty and students across disciplines to ask for suggested items to develop an endowed LGBTQIA+ collection. Outreach was performed via email to faculty and student clubs, and by attending campus facilities, events and committees. Assessment reviewed the collection’s item count and circulation reports before and after outreach.

Findings

Purchasing items to develop a collection does not always need to be the result of one librarian’s research. Engaging the campus community in the expansion of the endowed LGBTQIA+ collection resulted in substantial growth of items in the collection, as well as substantial growth in the collection’s circulation. Involving faculty and students from multiple disciplines in the suggestion process is one way to build and ensure a collection is relevant to a variety of interests, with an added result of increased circulation.

Originality/value

This approach is a unique example of how to use low-stakes engagement to discover items to purchase for a large endowment while increasing interest and circulation of the collection. The case study also explores how to embark on collection development in ways that effectively and sustainably reach beyond one academic discipline. Yet, the authors believe this study’s examples could also be used successfully within a single discipline.
Corporate strategy, political contributions and corporate risk-taking
Authors: Halari Anwar , Ahmad Sardar , Ullah Subhan , Amankwah-Amoah Joseph
Published: April 2023

Purpose

Despite the importance and prevalence of corporate political activities in modern organizations, there remains limited insight on the potential relationship between political contributions and companies’ risk-taking activities. This study aims to examine the relationship between monetary political contributions of firms and corporate risk-taking activities in the context of unstable political and economic environments.

Design/methodology/approach

The authors use a two-step system GMM estimation to investigate the subject using a cross-country sample of 307 firms from 22 countries covered over 2002–2017. In line with previous studies, the authors control for various corporate governance mechanisms, firm-level factors and country-level characteristics.

Findings

The findings demonstrate that firms that make monetary political contributions exhibit lower levels of risk as measured by different proxies for risks, namely, systematic, idiosyncratic and total risk.

Practical implications

The results suggest that political contributions can be a useful mechanism to mitigate risk exposure. Also, the use of different risk measures and other factors for robustness fosters a better understanding of political connectedness in a more contextualized and dynamic manner.

Originality/value

This study seeks to contribute to the debate surrounding corporate strategy, political connectedness and corporate risk-taking by using actual monetary political contributions as an explicit measure of political connection. This study furthers scholarly understanding on the dynamics of corporate political activities using political contributions in monetary terms as a measure of political connectedness and its impact on risk-taking. Furthermore, the authors explore this topic using insights from nonmarket strategy literature and studies on political contributions.