bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic molecular fragmentation by evolutionary optimisation
Authors: Yu Fiona C. Y. , Vallejo Jorge L. Gálvez , Barca Giuseppe M. J. 
Published: August 2024

AbstractMolecular fragmentation is an effective suite of approaches to reduce the formal computational complexity of quantum chemistry calculations while enhancing their algorithmic parallelisability. However, the practical applicability of fragmentation techniques remains hindered by a dearth of automation and effective metrics to assess the quality of a fragmentation scheme. In this article, we present the Quick Fragmentation via Automated Genetic Search (QFRAGS), a novel automated fragmentation algorithm that uses a genetic optimisation procedure to generate molecular fragments that yield low energy errors when adopted in Many Body Expansions (MBEs). Benchmark testing of QFRAGS on protein systems with less than 500 atoms, using two-body (MBE2) and three-body (MBE3) MBE calculations at the HF/6-31G* level, reveals mean absolute energy errors (MAEE) of 20.6 and 2.2 kJ $$\hbox {mol}^{-1}$$mol-1, respectively. For larger protein systems exceeding 500 atoms, MAEEs are 181.5 kJ $$\hbox {mol}^{-1}$$mol-1for MBE2 and 24.3 kJ $$\hbox {mol}^{-1}$$mol-1for MBE3. Furthermore, when compared to three manual fragmentation schemes on a 40-protein dataset, using both MBE and Fragment Molecular Orbital techniques, QFRAGS achieves comparable or often lower MAEEs. When applied to a 10-lipoglycan/glycolipid dataset, MAEs of 7.9 and 0.3 kJ $$\hbox {mol}^{-1}$$mol-1were observed at the MBE2 and MBE3 levels, respectively.Scientific ContributionThis Article presents the Quick Fragmentation via Automated Genetic Search (QFRAGS), an innovative molecular fragmentation algorithm that significantly improves upon existing molecular fragmentation approaches by specifically addressing their lack of automation and effective fragmentation quality metrics. With an evolutionary optimisation strategy, QFRAGS actively pursues high quality fragments, generating fragmentation schemes that exhibit minimal energy errors on systems with hundreds to thousands of atoms. The advent of QFRAGS represents a significant advancement in molecular fragmentation, greatly improving the accessibility and computational feasibility of accurate quantum chemistry calculations.
Muscle degeneration in aging Drosophila flies: the role of mechanical stress
Authors: Chechenova Maria , McLendon Lilla , Dallas Bracey , Stratton Hannah , Kiani Kaveh , Gerberich Erik , Alekseyenko Alesia , Tamba Natasya , An SooBin , Castillo Lizzet , Czajkowski Emily , Talley Christina , Brown Austin , Bryantsev Anton L. 
Published: August 2024

AbstractMuscle wasting is a universal hallmark of aging which is displayed by a wide range of organisms, although the causes and mechanisms of this phenomenon are not fully understood. We used Drosophila to characterize the phenomenon of spontaneous muscle fiber degeneration (SMFD) during aging. We found that SMFD occurs across diverse types of somatic muscles, progresses with chronological age, and positively correlates with functional muscle decline. Data from vital dyes and morphological markers imply that degenerative fibers most likely die by necrosis. Mechanistically, SMFD is driven by the damage resulting from muscle contractions, and the nervous system may play a significant role in this process. Our quantitative model of SMFD assessment can be useful in identifying and validating novel genetic factors that influence aging-related muscle wasting.
Signaling pathways activated and regulated by stem cell-derived exosome therapy
Authors: Li Ding , Li Danni , Wang Zhao , Li Jiaojiao , Shahzad Khawar Ali , Wang Yanhong , Tan Fei 
Published: August 2024

AbstractStem cell-derived exosomes exert comparable therapeutic effects to those of their parental stem cells without causing immunogenic, tumorigenic, and ethical disadvantages. Their therapeutic advantages are manifested in the management of a broad spectrum of diseases, and their dosing versatility are exemplified by systemic administration and local delivery. Furthermore, the activation and regulation of various signaling cascades have provided foundation for the claimed curative effects of exosomal therapy. Unlike other relevant reviews focusing on the upstream aspects (e.g., yield, isolation, modification), and downstream aspects (e.g. phenotypic changes, tissue response, cellular behavior) of stem cell-derived exosome therapy, this unique review endeavors to focus on various affected signaling pathways. After meticulous dissection of relevant literature from the past five years, we present this comprehensive, up-to-date, disease-specific, and pathway-oriented review. Exosomes sourced from various types of stem cells can regulate major signaling pathways (e.g., the PTEN/PI3K/Akt/mTOR, NF-κB, TGF-β, HIF-1α, Wnt, MAPK, JAK-STAT, Hippo, and Notch signaling cascades) and minor pathways during the treatment of numerous diseases encountered in orthopedic surgery, neurosurgery, cardiothoracic surgery, plastic surgery, general surgery, and other specialties. We provide a novel perspective in future exosome research through bridging the gap between signaling pathways and surgical indications when designing further preclinical studies and clinical trials.
Long-term Compressive Strength Properties of Concrete Incorporating Admixtures: Outdoor Exposure Testing in a Coastal Environment
Authors: Lee Binna , Lee Jong-Suk , Ryou Jae-Suk 
Published: August 2024

AbstractIn this study, concrete specimens were fabricated based on domestically manufactured materials, and long-term exposure tests were conducted in a domestic coastal environment. This study analyzes the long-term compressive strength characteristics of concrete mixed with admixtures. The mixed materials used were divided into blast furnace slag and fly ash. The blast furnace slag and fly ash were, respectively, produced by replacing ~ 30% and ~ 15% of the cement. The compressive strength was measured at 28 day, 1 year, and 10 years of age and compared with that of ordinary concrete. In addition, the long-term compressive strength results obtained in this study were compared with those of concrete mixed with admixtures reported in the literature. The strengths of the ordinary specimen at 1 year and 10 years of age increased by ~ 10 MPa and ~ 22 MPa compared with those at 28 day of age. However, concrete mixed with admixtures yielded compressive strength increases of ~ 5 MPa and ~ 26 MPa at 1 year and 10 years of age, respectively, compared with those at 28 day of age. A comparison of the compressive strengths of concrete mixed with admixtures reported in the literature (based on age) and those obtained in this study showed that there was an initial strength difference in the range of 10–25%. However, the compressive strength at 10 years of age was almost similar to those reported in the literature with differences of less than 5%. These findings confirmed that when using pozzolanic admixtures, the development rate of the initial strength may vary owing to various factors; however, the long-term strength converges within a certain range.
Unveiling the link: hepatitis C virus and Parkinson’s disease
Authors: Eletreby Rasha , Elhady Eman , Shaheen Shaimaa , Hamza Iman , Hashem Ahmed 
Published: August 2024

Abstract
Background
Parkinson disease (PD) is one of the disabling neurological disorders. The etiology of Parkinson disease is still unknown. Hepatitis C virus is one of the neurotropic viruses which is incriminated in the pathogenesis of Parkinson disease. Hepatitis C virus might affect the dopaminergic neurons, affecting the advancement of PD.

Methods
This study is observational, cross-sectional study done on 2 phases: one phase on PD patients without history of HCV and another phase on HCV patients with no history of PD. 104 PD patient were tested for HCV antibodies and 40 HCV patients with various grades of liver fibrosis were assessed for early pre-motor symptoms of parkinsonism.

Results
Among patients with parkinsonism, HCV Abs testing was negative in all the studied patients. On the other hand, chronic HCV group included 40 patients, 27.5% were cirrhotic (11/40). Child C patients showed significantly higher percentages of non-motor parkinsonian symptoms, and regarding the HCV group, the majority (85%) of the patients show cognitive impairment, (27.5%) were at stage 1 of anxious mood, while half (50%) of the patients were at stage 1 of fatigue as evaluated by UPDRS Score. Cirrhosis was a significant factor for having non-motor (early) parkinsonism.

Conclusion
Here we show that advanced cirrhosis is associated with a variety of neurological symptoms including parkinsonian, which needs awareness for better preventive and therapeutic measures for early treatment of hepatitis avoiding the occurrence of cirrhosis, which can lead to parkinsonism.
The biliary tree musketeers: cholangiocarcinoma – one name for all, but at least three different diseases with distinct targets
Authors: Marins Lidiane Vieira , Moniz Camila Motta Venchiarutti , Freire Cecília Souza , Campos Antonio Hugo José Fróes Marques 
Published: August 2024

AbstractCholangiocarcinoma, a malignant neoplasm of the biliary system, poses a significant challenge in clinical practice due to its increasing incidence and diagnostic and therapeutic complexity. This review addresses the epidemiological aspects, risk factors, and classification of this disease. We examine advances in histological diagnosis, highlighting essential criteria for accurate assessment. Additionally, we discuss standard treatment approaches and their efficacy, alongside the latest innovations in therapy, including emerging biomarkers and targeted therapies. By providing a comprehensive overview of these topics, this article aims to enhance understanding and guide the pathological diagnosis and clinical management of this devastating disease.
Pediatric Papillary Thyroid Carcinoma: Outcomes After Surgery Without Adjuvant Radioactive Iodine
Authors: Castellanos Luz E , Zafereo Mark E , Sturgis Erich M , Wang Jennifer R , Ying Anita K , Waguespack Steven G 
Published: August 2024

Abstract

Context
Pediatric papillary thyroid carcinoma (PTC) is usually treated with total thyroidectomy followed by radioactive iodine (RAI). Recently, RAI has been used more selectively based on surgical pathology and postoperative dynamic risk stratification (DRS).

Objective
To describe patients with pediatric PTC not initially treated with RAI and their disease outcomes.

Methods
This was an ambispective study at a tertiary cancer center of patients &lt; 19 years diagnosed from January 1, 1990, to December 31, 2021, with stage 1 PTC who intentionally were not treated with RAI within a year of diagnosis. We assessed clinical characteristics, management, and disease outcomes using DRS.

Results
Of 490 PTC patients, we identified 93 eligible patients (median age at diagnosis 16 years; 87% female), including 46 (49%) with cervical lymph node metastases. Initial management included total thyroidectomy ± neck dissection (n = 69, 75%), lobectomy ± neck dissection (n = 20, 21%), or a Sistrunk procedure for ectopic PTC (n = 4, 4%). After a median follow-up of 5.5 years (range 1-26), most patients (85/93; 91%) remained disease-free with no further therapy. Persistent (n = 5) or recurrent (n = 3) disease was found in 9% of the entire cohort. Four patients ultimately received RAI, of which only 1 clearly benefitted, and additional surgery was performed or planned in 4 patients, 2 of whom had an excellent response at last follow-up.

Conclusion
Selected pediatric PTC patients, even those with lymph node metastases, may not require therapeutic 131I and can avoid the unnecessary risks of RAI while still benefitting from the excellent long-term outcomes that are well described for this disease.
Robotic-Assisted Obturator Nerve Repair: A Technical Report
Authors: Syal Arjun , Vazquez Sima , Novetsky Akiva P. , Pisapia Jared 
Published: August 2024

BACKGROUND AND IMPORTANCE:
Untreated obturator nerve injury may result in weakness in thigh adduction, decreased medial thigh sensation, and groin pain. A neurosurgeon may be consulted intraoperatively for repair. Although there are reports of obturator nerve injury and repair in the gynecologic surgery literature, there are few reports detailing the specific steps of nerve repair after partial transection and the underlying principles of nerve coaptation, especially in the robotic-assisted setting.

CLINICAL PRESENTATION:
A partial transection of the right obturator nerve was noted in a patient undergoing total laparoscopic hysterectomy, bilateral salpingo-oophorectomy, and lymph node dissection using the da Vinci robot. Sutures were placed in the epineurium of the cut nerves to realign the fascicles. A porcine wrap was placed around the coaptation site and covered with fibrin glue. The right lower extremity was passively ranged to ensure no tension was present across the repair site. The patient had loss of right leg adduction after surgery, but she recovered full motor function 5 months after surgery with no numbness or pain.

CONCLUSION:
The current report describes a repair strategy for partial-thickness obturator nerve injury in the setting of a laparoscopic surgery. Working in a multidisciplinary fashion, the tenets of nerve repair may be applied to robotic-assisted cases of obturator nerve injury, resulting in neurologic recovery.
Suprasellar Anterior-Posterior Diameter Optimizes the Use of Intraoperative MRI in Patients Undergoing Endoscopic Pituitary Surgery
Authors: Hannan Cathal John , Daousi Christina , Radon Mark , Gilkes Catherine E. 
Published: August 2024

BACKGROUND AND OBJECTIVES:
Intraoperative MRI (iMRI) has been demonstrated to improve the extent of resection of pituitary neuroendocrine tumors resected using endoscopic endonasal approaches. We sought to establish if preoperative clinicoradiological parameters could be used to predict which patients are most likely to benefit from iMRI and thus allow more efficient use of this technology.

METHODS:
A prospectively maintained surgical database of all endoscopic pituitary tumor resections with iMRI guidance performed between May 2017 and September 2023 was accessed. Data were collected on clinical and radiological parameters that may predict reintervention after iMRI. Logistic regression models were constructed to assess the relationship between predictor variables and reintervention after iMRI.

RESULTS:
Seventy-three patients were included in the study. After review of the iMRI, 24/73 (33%) patients underwent surgical reintervention. The combined rate of gross total resection/near total resection was 64/73 (88%). The rate of biochemical cure of endocrine disease after surgery for a hormonally active tumor was 15/21 (71%). On univariate logistic regression analysis, the only factor significantly associated with reintervention after iMRI was the suprasellar anterior-posterior diameter (odds ratio 1.1, 95% CI 1.01-1.2, P = .030).

CONCLUSION:
Suprasellar anterior-posterior diameter ≥15 mm predicts the requirement for reintervention after endoscopic resection of pituitary neuroendocrine tumor. Use of this easily obtained radiological parameter will allow iMRI to be used in those patients who are most likely to benefit.
Transcirculation Approaches to Endovascular Flow Diversion of Intracranial Aneurysms: A Systematic Review With Technical Considerations
Authors: Covell Michael M. , Palepu Chandrasekhar , Sioutas Georgios S. , Stirrat Thomas P. , Prvulovic Stefan T. , Patel Saarang , Kandregula Sandeep , Burkhardt Jan-Karl , Srinivasan Visish M. 
Published: August 2024

BACKGROUND AND OBJECTIVES:Flow diversion (FD) of intracranial aneurysms (IAs) is an increasingly used and efficacious treatment modality. Transcirculation approaches, or approaches that cross the contralateral or anteroposterior arterial supply before reaching a target vessel, have been used to treat cerebrovascular pathologies when traditional approaches are unsuitable or require intraoperative complication management. This study sought to review IAs treated with FD using a transcirculation approach to determine the technique's safety and efficacy.METHODS:A systematic review of the PubMed, Scopus, Web of Science, and Embase databases was completed per Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Studies were included if they described transcirculation approaches in adult patients with IAs undergoing FD. Outcomes of interest included intraoperative complications and aneurysm occlusion rates.RESULTS:Twelve studies with 19 patients (N = 19, mean age = 54.1 y, 89.5% female) were identified. Wide-necked (N = 5, 26.3%) and saccular (N = 5, 26.3%) aneurysms were most represented, while 57.9% (N = 11) of aneurysms were unruptured and 15.8% (N = 3) of aneurysms were ruptured. The mean aneurysm sac and neck size were 16.9 mm and 11.9 mm, respectively. The most commonly deployed flow diverter was the Pipeline Embolization Device (N = 14, 73.9%). Successful FD (complete occlusion and/or good wall apposition) was recorded in 84.6% of qualifying patients with follow-up data, while 2 patients (15.4%) developed an intraoperative carotid-cavernous fistula.CONCLUSION:Transcirculation approaches to FD offer neurointerventionalists a safe and efficacious method for device deployment, rescue scenarios, and challenging anatomy. Prospective studies may determine the most appropriate indications for transcirculation approaches to FD, while novel, lower profile devices may improve its technical feasibility and safety.
Time to Elicit Physiological and Exertional Vigorous Responses from Daily Living Activities: Setting Foundations of an Empirical Definition of VILPA
Authors: AHMADI MATTHEW N. , HOLTERMANN ANDREAS , TUDOR-LOCKE CATRINE , KOSTER ANNEMARIE , JOHNSON NATHAN , CHAU JOSEPHINE , WEI LE , SABAG ANGELO , MAHER CAROL , THØGERSEN-NTOUMANI CECILIE , STAMATAKIS EMMANUEL 
Published: August 2024

ABSTRACT

Purpose
Vigorous intermittent lifestyle physical activity (VILPA) are bursts of incidental vigorous activity that occur during day-to-day activities outside of the exercise-domain. Vigorous intermittent lifestyle physical activity has shown promise in lowering risk of mortality and chronic disease. However, there is an absence of an empirically derived definition. Using physiological and effort-based metrics commonly used to define vigorous intensity, we investigated the minimum time needed to elicit physiological and perceived exertion responses to standardized activities of daily living.

Methods
Seventy adults (age = 58.0 ± 9.6 yr; 35 female) completed 9 VILPA activities of daily living in a randomized order, which included fast walking, fast incline walking, stair climbing, stationary cycling, and carrying external weight equal to 5% and 10% of body weight. Metabolic rate (by continuous indirect calorimetry), heart rate (telemetry) and perceived effort (Borg Scale) were measured during exercise. Time to reach VILPA was assessed using %V̇O2max, %HRmax, and rating of perceived exertion thresholds.

Results
The mean time to elicit VILPA ranged from 65 to 95 s (mean ± sd = 76.7 ± 3.8 s) for %V̇O2max, 68 to 105 s (mean ± sd = 82.8 ± 6.8 s) for %HRmax, and 20 to 60 s (mean ± sd = 44.6 ± 6.7 s) for rating of perceived exertion. For each of the three indices, there was no difference in the time to elicit VILPA responses by sex or age (P > 0.08), and times were also consistent between activities of daily living tasks. For example, for females and males, the average time to elicit vigorous responses while walking on a flat surface was 85.8 s (±16.9 s) and 80 s (±13.9 s), respectively, and for stair climbing while carrying 10% of body weight the duration was 78.4 s (±17.6 s) and 76.9 (±17.7 s).

Conclusions
When participants undertook activities of daily living, VILPA elicited a physiological response at an average of 77 to 83 s for %V̇O2max and %HRmax, and 45 s for perceived exertion. The absence of a difference in the time to reach VILPA between sex and age suggests that a consistent behavioral VILPA translation can be used in interventions and population-based studies designed to assess the health effects of incidental physical activity.
Exercise Intolerance in McArdle Disease: A Role for Cardiac Impairment? A Preliminary Study in Humans and Mice
Authors: SANTOS-LOZANO ALEJANDRO , BORAITA ARACELI , VALENZUELA PEDRO L. , SANTALLA ALFREDO , VILLARREAL-SALAZAR MÓNICA , BUSTOS ASUNCIÓN , ALEJO LIDIA B. , BARRANCO-GIL DAVID , MILLÁN-PARLANTI DANIELA , LÓPEZ-ORTIZ SUSANA , PEÑÍN-GRANDES SAúL , ORELLANA JOSé NARANJO , FIUZA-LUCES CARMEN , GáLVEZ BEATRIZ G. , GARCÍA-FERNáNDEZ MIGUEL ÁNGEL , PINÓS TOMÀS , LUCIA ALEJANDRO 
Published: August 2024

ABSTRACT

Introduction
Whether cardiac impairment can be fully discarded in McArdle disease—the paradigm of “exercise intolerance,” caused by inherited deficiency of the skeletal muscle–specific glycogen phosphorylase isoform (“myophosphorylase”)—remains to be determined.

Methods
Eight patients with McArdle disease and seven age/sex-matched controls performed a 15-min moderate, constant-load cycle-ergometer exercise bout followed by a maximal ramp test. Electrocardiographic and two-dimensional transthoracic (for cardiac dimension’s assessment) and speckle tracking (for left ventricular global longitudinal strain (GLS) assessments) echocardiographic evaluations were performed at baseline. Electrocardiographic and GLS assessments were also performed during constant-load exercise and immediately upon maximal exertion. Four human heart biopsies were obtained in individuals without McArdle disease, and in-depth histological/molecular analyses were performed in McArdle and wild-type mouse hearts.

Results
Exercise intolerance was confirmed in patients (“second wind” during constant-load exercise, −55% peak power output vs controls). As opposed to controls, patients showed a decrease in GLS during constant-load exercise, especially upon second wind occurrence, but with no other between-group difference in cardiac structure/function. Human cardiac biopsies showed that all three glycogen phosphorylase—myophosphorylase, but also liver and especially brain—isoforms are expressed in the normal adult heart, thereby theoretically compensating for eventual myophosphorylase deficiency. No overall histological (including glycogen depots), cytoskeleton, metabolic, or mitochondrial (morphology/network/distribution) differences were found between McArdle and wild-type mouse hearts, except for lower levels of pyruvate kinase M2 and translocase of outer-membrane 20-kDa subunit in the former.

Conclusions
This study provides preliminary evidence that cardiac structure and function seem to be preserved in patients with McArdle disease. However, the role for an impaired cardiac contractility associated with the second wind phenomenon should be further explored.