bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison
Authors: Guo Zhengyang , Wang Yang , Ou Guangshuo 
Published: February 2024

Abstract

Motivation
Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited.

Results
In this article, we have developed the align distance matrix with scale (ADAMS) pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy.

Availability
ADAMS can be download and used as a python package from Python Package Index (PyPI): adams · PyPI. Source code and other materials are available from young55775/ADAMS-developing (github.com). An online server is available: Bseek Search Server (cryonet.ai)
Comparison of the clinical efficacy of topical tretinoin 0.05% cream and tacrolimus 0.1% ointment plus iontophoresis in the management of palmoplantar psoriasis
Authors: Bubna Aditya Kumar 
Published: February 2024

Abstract

Background
Palmoplantar psoriasis (PPP) is a localized variant of psoriasis that may be resistant to topical therapy, owing to the poor penetrability of topical agents at this anatomical site. Modalities that enhance localized cutaneous delivery of drugs could help to solve this problem. Iontophoresis is one such procedure that augments transdermal drug delivery, thus enabling better and expeditious therapeutic outcomes.

Objective
To compare the therapeutic efficacy and safety of iontophoresis with tretinoin 0.05% cream and tacrolimus 0.1% ointment in treating patients with PPP.

Methods
Sixty patients with PPP (28 males and 32 females, age range 8–76 years) were enrolled and randomly assigned to one of two groups comprising 30 patients each. One group (12 males and 18 females) received iontophoresis with tretinoin 0.05% cream; the other (16 males and 14 females) received iontophoresis treatment with tacrolimus 0.1% ointment. Both groups received treatment weekly from baseline until 4 weeks and then fortnightly at weeks 6 and 8. Clinical images were taken at each visit and improvement of psoriasis was evaluated using the erythema, scaling, induration and fissuring (ESIF) score. The percentage reduction in ESIF score was also assessed on completion of treatment and the grade of improvement noted for each patient.

Results
Twenty-seven patients in the iontophoresis with tretinoin 0.05% cream group and 29 in the iontophoresis treatment with tacrolimus 0.1% ointment group completed the study. The mean (SD) ESIF score in the former decreased significantly from 8.7 (2) at baseline to 3.2 (1.7) at the study endpoint (P &lt; 0.001). Similarly, in the latter group, there was a substantial reduction in mean (SD) ESIF score from 8.2 (1.9) at baseline to 3.3 (1.1) at the study end (P &lt; 0.001). No significant adverse effects were encountered in either treatment arm.

Conclusions
Iontophoresis using tretinoin and tacrolimus was found to be effective and safe for the treatment of PPP. Although iontophoresis with tretinoin showed slightly better results than with tacrolimus, these were not statistically significant.
Morphometric analysis of chronicity on kidney biopsy: a useful prognostic exercise
Authors: Asghar Muhammad S , Denic Aleksandar , Rule Andrew D 
Published: February 2024

ABSTRACT
Chronic changes on kidney biopsy specimens include increasing amounts of arteriosclerosis, glomerulosclerosis, interstitial fibrosis and tubular atrophy, enlarged nephron size, and reduced nephron number. These chronic changes are difficult to accurately assess by visual inspection but are reasonably quantified using morphometry. This review describes the various patient populations that have undergone morphometric analysis of kidney biopsies. The common approaches to morphometric analysis are described. The chronic kidney disease outcomes associated with various chronic changes by morphometry are also summarized. Morphometry enriches the characterization of chronicity on a kidney biopsy and this can supplement the pathologist's diagnosis. Artificial intelligence image processing tools are needed to automate the annotations needed for practical morphometric analysis of kidney biopsy specimens in routine clinical care.
“Prince Charming with an Erection”: The Sensational Pleasures of the Bonkbuster
Authors: Burge Amy , McAlister Jodi , Ireland Charlotte 
Published: February 2024

Abstract
The bonkbuster—an explosively popular genre of women’s writing in the 1970s, 1980s, and 1990s—had an interesting resurgence in 2023. UK Prime Minister Rishi Sunak claims to be a fan of bonkbuster author Jilly Cooper, whose novel Rivals (1988) is being adapted for television. But what is a bonkbuster? And how is it different from the genre with which it is most associated: the romance novel? In this article, the first to analyze the bonkbuster in detail, we focus on two concerns common to both forms—sex and relationships—and explore how bonkbusters revel in their own “badness.” We argue that the pleasures of a bonkbuster are rooted in their sensationalism and their ironic potential.
Periprocedural myocardial infarction and injury
Authors: Spagnolo Marco , Occhipinti Giovanni , Laudani Claudio , Greco Antonio , Capodanno Davide 
Published: February 2024

AbstractPeriprocedural myocardial infarction (PMI) and injury, pertinent to both cardiac and non-cardiac procedures, have gained increasing recognition in clinical practice. Over time, diverse definitions for diagnosing PMI have been developed and validated among patient populations undergoing coronary revascularization. However, this variety in definitions presents considerable challenges in clinical settings and complicates both the design and interpretation of clinical trials. The necessity to accurately diagnose PMI has spurred significant interest in establishing universally accepted and prognostically meaningful thresholds for cardiac biomarkers elevation and supportive ancillary criteria. In fact, elevations in cardiac biomarkers in line with the 4th Universal Definition of Myocardial Infarction, have been extensively confirmed to be associated with increased mortality and cardiovascular events. In the context of non-coronary cardiac procedures, such as Transcatheter Aortic Valve Implantation, there is a growing acknowledgment of both the high incidence rates and the adverse impact of PMI on patient outcomes. Similarly, emerging research underscores the significance of PMI and injury in non-cardiac surgery, highlighting the urgent need for effective prevention and risk management strategies in this domain.
Peak atrial longitudinal strain and risk stratification in moderate and severe aortic stenosis
Authors: Springhetti Paolo , Tomaselli Michele , Benfari Giovanni , Milazzo Salvatore , Ciceri Luca , Penso Marco , Pilan Matteo , Clement Alexandra , Rota Alessandra , Del Sole Paolo Alberto , Nistri Stefano , Muraru Denisa , Ribichini Flavio , Badano Luigi 
Published: February 2024

Abstract

Aims
We sought to investigate the association of left atrial strain with the outcome in a large cohort of patients with at least moderate aortic stenosis (AS).

Methods and results
We analysed 467 patients (mean age 80.6 ± 8.2 years; 51% men) with at least moderate AS and sinus rhythm. The primary study endpoint was the composite of all-cause mortality and hospitalizations for heart failure. After a median follow-up of 19.2 (inter-quartile range 12.5–24.4) months, 96 events occurred. Using the receiver operator characteristic curve analysis, the cut-off value of peak atrial longitudinal strain (PALS) more strongly associated with outcome was &lt;16% {area under the curve (AUC) 0.70 [95% confidence interval (CI): 0.63–0.78], P &lt; 0.001}. The Kaplan–Meier curves demonstrated a higher rate of events for patients with PALS &lt; 16% (log-rank P &lt; 0.001). On multivariable analysis, PALS [adjusted HR (aHR) 0.95 (95% CI 0.91–0.99), P = 0.017] and age were the only variables independently associated with the combined endpoint. PALS provided incremental prognostic value over left ventricular (LV) global longitudinal strain, LV ejection fraction, and right ventricular function. Subgroup analysis revealed that impaired PALS was also independently associated with outcome in the subgroups of paucisymptomatic patients [aHR 0.98 (95% CI 0.97–0.98), P = 0.048], moderate AS [aHR 0.92, (95% CI 0.86–0.98), P = 0.016], and low-flow AS [aHR 0.90 (95% CI 0.83–0.98), P = 0.020].

Conclusion
In our patients with at least moderate AS, PALS was independently associated with outcome. In asymptomatic patients, PALS could be a potential marker of sub-clinical damage, leading to better risk stratification and, potentially, earlier treatment.
Toroidal mantle flow beneath the NE termination of the Kuril–Kamchatka subduction zone from seismic anisotropy
Authors: Kaviani Ayoub , Rümpker Georg , Sens-Schönfelder Christoph , Komeazi Abolfazl , Shapiro Nikolai 
Published: February 2024

SUMMARY
This study presents the findings of a splitting analysis conducted on core-refracted teleseismic shear waves (SKS, SKKS and PKS, called together as XKS) and local shear waves, obtained from a dense seismological network spanning the Kamchatka Peninsula. The objective of the study is to examine the pattern of mantle flow beneath the study area through the investigation of seismic anisotropy. The peninsula is situated at the northeastern end of the Kuril–Kamchatka subduction zone, where the Kuril trench intersects with the western boundary of the Aleutian trench. The data set utilized in this study comprises waveform data from a dense network of seismic stations (99 broad-band and short-period stations for the local shear wave splitting analysis and 69 broad-band stations for the SKS splitting analysis). The seismograms were downloaded from publicly available data repositories including the IRIS Data Management Center and the GFZ Data Services (GEOFON program). The dense station coverage allows us to investigate the lateral variations in anisotropy, providing insights into the flow patterns within the mantle. The processing of the combined data sets of local shear wave and teleseismic XKS waves allowed us to partially decipher the source of anisotropy in the mantle. Small delay (splitting) times (∼0.35 s) observed from the local-S data suggest that anisotropy in the mantle wedge is relatively weak with lateral variations. Larger splitting times (∼1.1 s) observed for the XKS waves relative to local S suggest that the main part of splitting on the XKS waves occurs in the subslab mantle. On the other hand, the rotational pattern of seismic anisotropy observed by both the local S and XKS waves suggests the presence of a toroidal flow at the NE edge of the subducting slab, which affects both the mantle wedge and subslab mantle. For the regions away from the edge of the slab, the mantle flow seems to be governed mainly by the drag of the lithospheric plate over the underlying asthenosphere.
SARS-CoV-2 Variants Genotyping and Diagnostic Performance of a 2-Genes Detection Assay
Authors: Matheka Cyrus , Kilonzo Joshua , Mbugua Ephantus , Munshi Zubair , Nyasinga Justin , Gunturu Revathi , Njau Allan 
Published: February 2024

Abstract

Background
The emergence of the COVID-19 pandemic resulted in the unprecedented expansion of molecular testing technologies. This study aimed at evaluating the performance of the FluoroType® SARS-CoV-2 plus assay for SARS-CoV-2 detection as well as describing the detection of SARS-CoV-2 variants using the FluoroType® SARS-CoV-2 varID Q kit.

Methods
The study utilized 679 archived nasopharyngeal samples. Analytical performance and the diagnostic performance of the FluoroType® SARS-CoV-2 plus assay were determined using 320 samples and reference material. Variants identification on the FluoroType® SARS-CoV-2 varID Q assay was performed on 359 samples. The study was approved by the Aga Khan University Hospital Institutional Review Board.

Results
The FluoroType® SARS-CoV-2 plus assay’s limit of detection was verified as 1.2 copies/µL. The repeatability SD and %CV were 2.45 and 9.8% while reproducibility had an SD and %CV of 1.39 and 5.68%, respectively, for the RdRP gene. The positive and negative percent agreement were determined to be 99.4% (95% CI; 98.1%–100%) and 99.4% (95% CI; 98.2%–100%) respectively. In the variants identification, samples from the original wave had no mutations identified while 12.3%, 49%, and more than 90% of the samples during the Alpha, Delta, and Omicron waves, respectively, had detectable mutations.

Conclusions
The FluoroType® SARS-CoV-2 plus assay demonstrated analytical performance comparable to the reference method with a diagnostic sensitivity and specificity of &gt;99%. The FluoroType® SARS-CoV-2 varID Q assay achieved rapid detection of circulating variants.
Robotic-assisted minimally invasive repair surgery for progressive spondylolysis in a young athlete: a technical note
Authors: Yamashita Daisuke , Yamashita Kazuta , Sugiura Kosuke , Morimoto Masatoshi , Manabe Hiroaki , Tezuka Fumitake , Sairyo Koichi 
Published: February 2024

Abstract
Presently, the invasiveness of direct repair surgery for lumbar spondylolysis is relatively high. Thus, high school and junior high school students who play sports often cannot return to sports before graduation because of the invasiveness. The use of a robotic system enabled an accurate and minimally invasive procedure. Robotic-assisted minimally invasive direct pars repair surgery is useful for young patients with progressive spondylolysis.
(020) Comparing Postoperative Outcomes and Risk Factors for Patients Undergoing Partial vs Total Penectomy for Penile Carcinoma
Authors: Liu A , Kalidoss S , Yeaman C , Bryk D , Fustok J , Shelton T , Alhameedi H , Payakachat N , Khalil M , Raheem O 
Published: February 2024

Abstract

Introduction
The American Cancer Society estimates that 2,200 men develop penile cancer annually and 440 men will die from the disease. Partial penectomies (PP) and total penectomies (TP) are both performed for penile cancer in the United States. Compared to TP, PP is performed more frequently to preserve functional urinary outcomes.

Objective
To date TP and PP outcomes have not been compared, in this study we compared clinical characteristics and post-operative outcomes between TP and PP conducted between 2006-2016.

Methods
We conducted a retrospective review of penile cancer patients from National Surgical Quality Improvement Program (NSQIP) database for the years 2010-2016 using international classification of diseases clinical modification (ICD-CM) ninth revision codes. A total of 260 patients, 67 TP and 193 PP patients, were included.

Results
Partial penectomy patients were less likely to be transferred patients (7.3% vs 20.9%, p=0.002), less likely to be suffering from diabetes (25.9% vs 40.3%, p=0.026), and were more likely to have preoperative laboratory values within normal limits. TP was associated with increased preoperative white blood cell count x109, preoperative white blood cell count &gt; 7.5x109 (p&lt;0.001), preoperative hematocrit (p&lt;0.001). PP patients were, in contrast, shown to have higher pre-operative creatinine levels (p=.037) and lower platelet levels than TP patients (p=.045). PP patients had shorter operation times (78.8 vs 145.5 min, p&lt;0.001). PP patients also had decreased levels of inpatient stay length (1.67 vs 4.31, p&lt;0.001), any 30-day post-surgery complication (7% vs 31%, p&lt;0.001), deep incisional surgical site infection (0.5% vs 6% p=0.017), wound disruption (0.5% vs 6.0%p=0.017), intraoperative or postoperative transfusion (1.6% vs 7.5%, p=0.029), and sepsis (0.5% vs 7.5%, p=0.005), when compared to patients who underwent TP. TP patients displayed a significantly greater number of concurrent surgical procedures (p&lt;0.001), when compared to PP patients. There was no information on urinary, sexual, and erectile outcomes in the database.

Conclusions
PP is associated with fewer post-operative complications, shorter surgeries, shorter hospital stays, and fewer concurrent surgical procedures. Total penectomy is associated with a greater proportion of patients suffering from comorbid conditions, suggesting that TP patients are at higher risk for post-surgical complications and longer hospital stays. There is a gap in reported data pertaining to post-operative sexual function and erectile outcomes for PP at a national level.

Disclosure
No.
(031) Effects of Gender Affirming Hormone Therapy vs. Puberty Blockers on Sexual Function and Desire
Authors: Finegan J , Anger J , Okamuro K , Marino-Kibbee B , Newfield R , Marinkovic M 
Published: February 2024

Abstract

Introduction
Many transgender and nonbinary (TGNB) individuals seek out puberty blockers (PB) to stop the progression of unwanted changes from endogenous puberty and/or gender affirming hormone therapy (GAHT) to aid in their medical transition. There has been limited research assessing the effect of these hormone therapies on sexual function and desire, especially in comparing GAHT and PB+GAHT.

Objective
Our aim was to compare the effect of GAHT and PB+GAHT on sexual function and desire of TGNB individuals during or following hormone therapy.

Methods
We performed an IRB approved two institutional study on the effect of GAHT and/or PB on sexual function and desire in adults. The GAHT group (n=12) included individuals who started GAHT (estrogen or testosterone) &gt;18 years old. The PB group (n=10) included subjects with current or past history of GnRH agonist use (&gt;10 years old). Enrolled subjects completed the validated Changes in Sexual Functioning Questionnaire (CSFQ). The CSFQ was validated in adults to assess medication-related changes in sexual functioning. The questionnaire is specific to sex assigned at birth with a male and female version. The answers were scored in total and separated into sexual function and sexual desire subscales. Scores in each group were compared using unpaired t-tests.

Results
A total of 22 TGNB (16 assigned male at birth and 6 assigned female at birth: 14 transgender women, 5 transgender men, 3 non-binary) subjects ages 18-25 completed the CSFQ about the effect hormone therapy had on sexual function and desire. There was no difference between groups in total scores (t = 0.8, p = 0.05) or in categories of sexual function (t = 0.3, p = 0.05) and desire (t = 0.8, p = 0.05). There were an equal number of participants in both groups whose results showed sexual dysfunction in total (n=2 per group) and in categories of sexual function (n=7 per group) and desire (n=3 per group). The cause of their dysfunction is unclear at this time and is to be investigated in the future. Interestingly, despite meeting quantitative criteria for sexual dysfunction, 6 participants answered that their sexual life brings them “much” or “great” enjoyment or pleasure.

Conclusions
Based on our results, while there were &gt;70% of subjects in each group with impaired sexual function, there were no differences in effect on sexual function and desire between subjects on GAHT vs. PB+GAHT. Additionally, the scores for both groups did not differ substantially from scores of cisgender individuals (Keller, et al 2006). In fact, both the GAHT and PB+GAHT groups scored higher on average in the sexual desire category compared to cisgender individuals. Prospective data collection will help us clarify further whether starting age of pubertal blockers and hormone therapy affects sexual function and desire.

Disclosure
No.
(032) Experience with Gender Affirming Hormones and Puberty Blockers: A Qualitative Analysis of Sexual Function
Authors: Finegan J , Marinkovic M , Okamuro K , Marino-Kibbee B , Newfield R , Anger J 
Published: February 2024

Abstract

Introduction
Gender affirming hormone therapy (GAHT) is part of the transition for many transgender and nonbinary (TGNB) individuals. Additionally, it has become increasingly more common for TGNB youth to receive puberty blockers (GnRH agonist) to halt the pubertal progression. There have been few studies investigating sexual function and desire either during or after puberty blockers (PB) and/or GAHT.

Objective
Our aim was to qualitatively evaluate the sexual experience of TGNB individuals during or following PB and/or GAHT, and outline any potential differences between the two groups.

Methods
We performed an IRB approved two institutional study on the effect of PB and/or GAHT on sexual function and desire. The GAHT group (n=16): individuals who started GAHT (estrogen or testosterone) &gt;18 years. The PB+GAHT group (n=10): subjects with current or past GnRH agonist use +GAHT. All 26 enrolled subjects were interviewed using an open-ended topical guide. Qualitative analysis was performed by hand coding the interview transcripts using Constructivist Grounded Theory qualitative methods.

Results
A total of 26 TGNB (20 assigned male at birth, 6 assigned female at birth: 18 transgender women, 5 transgender men, 3 non-binary) subjects ages 18-25y were interviewed about the effect of PB and/or GAHT on their sexual function and desire. Our analysis uncovered several themes that were consistent between groups (Table 1).

Conclusions
Themes were similar for both groups. Half the participants in each group reported feeling no regrets regarding hormone therapy, and the other half reported that they wished they had started hormones sooner. Two notable differences were identified between groups: those on PB+GAHT reported “less dysphoria” as a positive change in sexual desire, and the GAHT group reported more enjoyable sexual experiences since being on hormones. Interestingly, results did not reveal any significant differences between groups. The most prominent theme that arose in both groups was that the positive changes in sexual function and desire outweighed any negative changes that arose.

Disclosure
No.