bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking graph representation learning algorithms for detecting modules in molecular networks
Authors: Song Zhiwei , Baur Brittany , Roy Sushmita 
Published: August 2023

Background: A common task in molecular network analysis is the detection of community structures or modules. Such modules are frequently associated with shared biological functions and are often disrupted in disease. Detection of community structure entails clustering nodes in the graph, and many algorithms apply a clustering algorithm on an input node embedding. Graph representation learning offers a powerful framework to learn node embeddings to perform various downstream tasks such as clustering. Deep embedding methods based on graph neural networks can have substantially better performance on machine learning tasks on graphs, including module detection; however, existing studies have focused on social and citation networks. It is currently unclear if deep embedding methods offer any advantage over shallow embedding methods for detecting modules in molecular networks. Methods: Here, we investigated deep and shallow graph representation learning algorithms on synthetic and real cell-type specific gene interaction networks to detect gene modules and identify pathways affected by sequence nucleotide polymorphisms. We used multiple criteria to assess the quality of the clusters based on connectivity as well as overrepresentation of biological processes. Results: On synthetic networks, deep embedding based on a variational graph autoencoder had superior performance as measured by modularity metrics, followed closely by shallow methods, node2vec and Graph Laplacian embedding. However, the performance of the deep methods worsens when the overall connectivity between clusters increases. On real molecular networks, deep embedding methods did not have a clear advantage and the performance depended upon the properties of the graph and the metrics. Conclusions: Deep graph representation learning algorithms for module detection-based tasks can be beneficial for some biological networks, but the performance depends upon the metrics and graph properties. Across different network types, Graph Laplacian embedding followed by node2vec are the best performing algorithms.
Morphological, structural, chemical, vibrational, thermal, pasting, and functional changes in pea starch during germination process
Authors: Lucas-Aguirre Juan Carlos , Quintero-Castaño Víctor Dumar , Castañeda-Cano Luisa Fernanda , Rodríguez-García Mario Enrique 
Published: August 2023

Background: Changes in the structural and physicochemical properties of pea starch could be significantly affected by germination treatment, which can provide a theoretical basis for promoting the use of this starch in the food industry. Methods: This work aims to evaluate the effect of germination time on the structural, thermal, rheological and functional properties of pea starches to determine their potential in the production of fermented beverages. The physicochemical changes during the germination process of peas and native and germinated starch granules were evaluated. Results: For germination critical time was 0.985 days, with 95% of germinated grains. The starch grains did not undergo any morphological change during the germination process as seen in the scanning electron microscopy images, indicating the absence of the α and ß - amylases responsible for the starch splitting. The X-ray patterns revealed that the crystalline structures of pea starch with and without germination were unchanged and contained by hexagonal and orthorhombic glucopyranose crystals. The viscosity profiles of the starches do not show significant changes; the most representative change is the increase in the gelatinization onset temperature of the paste from germinated starches compared to native starch. The functional properties of starches showed generally low values, with statistically significant differences between water absorption index, water solubility index, and starch swelling power and germination time. Conclusions: In general terms, it can be concluded that lentil starch does not undergo significant changes in its physicochemical and functional integrity with respect to the grain germination process.
A prospective assessment of gait kinematics and related clinical examination measures in cerebral palsy crouch gait
Authors: O'Sullivan Rory , French Helen , Horgan Frances 
Published: August 2023

Background While prospectively assessed crouch gait in cerebral palsy (CP) does not necessarily progress, prospective changes in clinical examination measures have not been reported. This study prospectively examined the association between selected clinical examination variables and change in crouch gait in a cohort with bilateral CP. Methods Inclusion criteria were a diagnosis of ambulant bilateral CP, knee flexion at mid-stance >19 0 and a minimum of two-years between gait analyses. The change in kinematic variables was assessed using Statistical Parameter Mapping (SPM) and changes in clinical measures using appropriate paired tests. Linear regression examined the association between progression of crouch and clinical examination variables. Results There was no mean change in crouch in 27 participants over 3.29 years. However, there was significant variability within this group. Clinical hamstring tightness (60.00 0 to 70.48 0, p<0.01) and external knee rotation during stance (SPM analysis, p<0.001) increased but there was no association between changes in clinical examination variables and changes in crouch (p-values 0.06 - 0.89). Conclusions This prospective study found no association between the changes in clinical examination variables and changes in crouch highlighting the likely multi-factorial aetiology of this gait pattern and the need for larger prospective studies. The variability crouch gait progression among the 27 participants highlights the pitfall of group mean values in such a heterogeneous population.
A 15-YEAR SURVIVAL ANALYSIS OF OXIDIZED ZIRCONIUM TOTAL KNEE ARTHROPLASTY
Authors: Fennelly Joseph , Santini Alasdair , Papalexandris Stylianos , Pope Jill , Yorke Joanne , Davidson John 
Published: August 2023

AbstractBackgroundOxidized zirconium (OxZr) has been introduced as an alternative bearing for femoral components in Total Knee Arthroplasty (TKA). It has a ceramic-like zirconium oxide outer layer with a low coefficient of friction. Early studies have found OxZr TKA to have a low incidence of early failure in young high demand patients. Currently no study has reported on the outcome of these implants beyond ten years.ObjectivesThe purpose of our study was to present an in-depth 15-year survival analysis of cemented Profix II OxZr TKA.Study Design & MethodsData was collected prospectively and survival analysis undertaken with multiple strict end points. Complication rates were recorded and patient reported outcomes were measured.Results617 Profix II OxZr TKAs were performed over four years. Forty-nine patients underwent reoperation. Aseptic tibial loosening was the most common cause of failure (32.7%) on average occurring 2.8 years post primary procedure. There was one recorded failure due to loosening of the zirconium femoral component. Revision rate at 15-years was 6.38%. Cumulative survivorship was 91.52% with failure considered to be reoperation for any reason. WOMAC score improved in 86% of patients by year 1. The average score improved by 21.2 points and met the standard for minimum clinically important difference.ConclusionsThis study presents the first 15-year survival analysis of cemented Profix II OxZr TKA. Our data supports current literature on the long-term survivorship of oxidised zirconium total knee replacements.
POLYETHYLENE BEARING WEAR OF THE OXFORD UNICOMPARTMENTAL KNEE ARTHROPLASTY: TEN-YEAR RESULTS OF A RANDOMIZED CONTROLLED TRIAL COMPARING CEMENTED AND CEMENTLESS FIXATION
Authors: Arthur Lachlan , Ghosh Priyanka , Mohammad Hasan , Campi Stefano , Murray David , Mellon Stephen 
Published: August 2023

AbstractIntroductionThe Oxford Unicompartmental Knee Replacement's (OUKR's) fully-congruent design minimises polyethylene wear. Consequently, wear is a rare failure mechanism. Phase-3 OUKR linear wear at 5 years was higher than previous OUKR phases, but very low compared to fixed-bearing UKRs. This study aimed to measure OUKR bearing wear at 10 years and investigate factors that may affect wear.MethodologyBearing thickness for 39 OUKRs from a randomised study was calculated using radiostereometric analysis at regular intervals up to 10 years. Data for 39 and 29 OUKRs was available at 5 and 10 years, respectively. As creep occurs early, wear rate was calculated using linear regression between 6 months and 10 years. Relationships between wear and patient factors, fixation method, Oxford Knee Score (OKS), bearing position, and component position were analysed.ResultsThe mean wear rate was 0.06mm/year. Fixation method, age, OKS, component size, and bearing size had no correlation with wear. A higher BMI was associated with lower wear (p=0.01). Bearings more than 4mm from the wall had significantly more wear (p=0.04) than those less than 4mm from the wall. There was a linear correlation between the femoral component contact area on the bearing and wear (p=0.04).ConclusionsPhase-3 bearing wear rate is constant, significantly higher than previous OUKR phases at 10 years, and may increase the risk of long-term bearing failure. To minimise complications associated with wear, size 4 bearings should be used in young patients and manufacturing bearings from more durable, highly crosslinked polyethylene should be studied.
REST: A PROSPECTIVE RANDOMIZED FEASIBILITY STUDY ASSESSING THE IMPACT OF A TAILORED SLEEP INTERVENTION IN PATIENTS UNDERGOING TOTAL KNEE ARTHROPLASTY
Authors: Bertram Wendy , Wylde Vikki , Glynn Joel , Penfold Chris , Burston Amanda , Johnson Emma , Rayment Dane , Howells Nick , White Simon , Gooberman-Hill Rachael , Whale Katie 
Published: August 2023

AbstractIntroductionThere is a need to develop approaches to reduce chronic pain after total knee replacement. There is an established link between disturbed sleep and pain. We tested the feasibility of a trial evaluating the clinical and cost-effectiveness of a pre-operative sleep assessment and complex intervention package for improving long-term pain after TKR.MethodologyREST was a feasibility multi-centre randomised controlled trial with embedded qualitative study and health economics. Participants completed baseline measures and were randomised to usual care or the intervention, a tailored sleep assessment and behavioural intervention package delivered by an extended scope practitioner three months pre-operatively with a follow-up call up at four-weeks. Patient reported outcomes were assessed at baseline, one-week pre-surgery, and 3-months post-surgery.Results57 patients were randomised and 20 had surgery within the study timelines. All patients allocated the intervention attended an appointment and most engaged with treatment. The intervention group reported improvements in sleep (Sleep Conditions Indicator) and neuropathic pain (painDETECT) scores. Participants found the sleep treatments and study processes to be acceptable. The mean cost of the intervention was estimated at £134.45 per patient.ConclusionThe feasibility study has shown that patient recruitment is feasible, engagement with and adherence to the intervention is high, and the intervention is acceptable to patients and clinicians. Preliminary findings show that the intervention group had improved sleep quality and had reduced levels of pre-operative neuropathic pain. This study has demonstrated that a full RCT is feasible and identified areas for improvement to optimize the trial design.
DOES OBESITY HAVE AN EFFECT ON PATIENT OUTCOMES AND PLATE SURVIVORSHIP IN HIGH TIBIAL OSTEOTOMY SURGERY? THE TOMOFIX ANATOMICAL MEDIAL HIGH TIBIAL PLATE
Authors: Nicholls Kate , Petsiou Dioni , Wilcocks Katharine , Shean Katharine , Anderson James , Vachtsevanos Leonidas 
Published: August 2023

AbstractIntroductionSurgery in patients with high body mass index (BMI) is more technically challenging and associated with increased complications post-operatively. Inferior clinical and functional mid-term results for high BMI patients undergoing high tibial osteotomy (HTO) relative to normal weight patients have been reported. This study discusses the clinical, radiological and functional outcomes of HTO surgery in patients with a high BMI.MethodThis is a retrospective study on patients undergoing HTO surgery using the Tomofix anatomical MHT plate between 2017 and 2022, with follow-up period of up to 5 years. The cohort was divided: non-obese (BMI <30 kg/m2) and obese (BMI>30 kg/m2). Pre and post operative functional scores were collected: Oxford Knee Score (OKS), EuroQol-5D and Tegner. Complications, plate survivorship and Mikulicz point recorded.Results32 HTO procedures; 19 patients BMI <30 (average 27.0) and 14 patients BMI >30 (average 36.1). In BMI<30 cohort, one readmission for investigation of venous thromboembolism, doppler negative; two complications: hinge fracture and stitch abscess. The five year survivorship of the plate was 100%. In BMI>30 cohort, one readmission for pulmonary embolism; one complication: hinge fracture. The 5 year survivorship of the plate was 93%, 1 conversion to unicompartmental knee replacement. The average OKS improvement was 17 and 18 for BMI <30 and >30 respectively. Mikulicz point change was identical.ConclusionThe Tomofix anatomical MHT plate achieves good outcomes and minimal complications irrespective of BMI. Reduced plate survivorship, thus earlier conversion may be required in the obese, however higher cohort numbers are needed to confirm this.
A REVISION ARTHROPLASTY NETWORK HAS SIGNIFICANTLY REDUCED EARLY RE-REVISION RATES FOLLOWING REVISION TOTAL KNEE ARTHROPLASTY COMPARED WITH THE REST OF ENGLAND: AN ANALYSIS OF THE EAST MIDLANDS SPECIALIST ORTHOPAEDIC NETWORK USING A NATIONAL ADMINISTRATIVE DATA SET
Authors: Bloch Benjamin , Berber Reshid , Matar Hosam , James Peter , Manktelow Andrew 
Published: August 2023

AbstractIntroductionRevision total knee arthroplasty (RTKA) is a complex procedure with higher rates of re-revision, complications and mortality compared to primary TKA. We report the effects of the establishment of a Revision Arthroplasty Network (The East Midlands Specialist Orthopaedic Network; EMSON).MethodologyThe Revision Arthroplasty Network was established in January 2015 and covered the Nottinghamshire and Lincolnshire areas of England. This comprises a collaborative weekly multidisciplinary meeting where upcoming RTKA procedures are discussed, and a plan agreed.Using the Hospital Episode Statistics database, RTKA procedures carried out between 2011 and 2018 from the five EMSON hospitals were compared to all other hospitals in England. Age, sex, and Hospital Frailty Risk scores were used as covariates.The primary outcome was re-revision surgery within 1 year of the index revision. Secondary outcomes were re-revision surgery within two years, any complication within one and two years and median length of stay.Results33,828 RTKA procedures were performed across England; 1,028 (3.0%) were conducted within EMSON. Re-revision rates within 1 year were 11.6% and 7.4% pre- and post-intervention respectively within the network. This compares to a pre-post change from 11.7% to 9.7% for the rest of England. In comparative interrupted time-series analysis, there was a significant immediate improvement in re-revision rates for EMSON hospitals compared to the rest of England at 1 year (p = 0.024) and 2 years (p=0.032).ConclusionRe-revision rates for RTKA improved significantly at one and two years with the introduction of EMSON, when compared to the rest of England.
FOCAL RESURFACING OF THE KNEE: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Mikova Ester , Kunutsor Setor , Butler Meg , Murray James 
Published: August 2023

AbstractIntroductionActive, middle-aged patients with symptomatic cartilage or osteochondral defects can find themselves in a treatment gap when they have failed conservative measures but are not yet eligible for conventional arthroplasty. Data from various cohort studies suggests that focal knee resurfacing implants such as HemiCAP, UniCAP, Episealer or BioBoly are cost-effective solutions to alleviate pain, improve function and delay or eliminate the need for conventional replacement. A systematic review and meta-analysis were conducted in order to(i) evaluate revision rates and implant survival of focal resurfacing; (ii) explore surgical complications; and (iii) evaluate various patient reported clinical outcome measures.MethodologyPubMED, Cochrane Library and Medline databases were searched in February 2022 for prospective and retrospective cohort studies evaluating any of the available implant types. Data on incidence of revision, complications and various patient reported outcome measures was sourced.ResultsA total of 24 unique studies were identified with a total of 1465 enrolled patients. A revision rate of 12.97% over a 5.9 year weighted mean follow-up period was observed across all implant types. However, in one series a Kaplan-Meir survival as high as 92.6% at a 10-year follow-up period was noted. A statistically significant improvement was documented across multiple subjective clinical outcomes scores. There was a low reported incidence of post-operative complications such as aseptic loosening or deep wound infection.ConclusionsFocal femoral resurfacing appears to be a viable treatment option for focal symptomatic chondral lesions in patients beyond biological reconstruction, with low revision rates and high patient satisfaction.
THE MENISCAL TEAR OUTCOME (METRO) STUDY: A PROSPECTIVE NATIONAL COHORT STUDY EXPLORING THE OUTCOMES OF PATIENTS WITH A MENISCAL TEAR
Authors: Ahmed Imran , Dhaif Fatema , Bowes Mike , Parsons Nicholas , Hutchinson Charles , Staniszewska Sophie , Price Andrew , Metcalfe Andrew 
Published: August 2023

AbstractIntroductionPrevious research has demonstrated no clinically significant benefit of arthroscopic meniscectomy in patients with a meniscal tear, however, patients included in these studies would not meet current treatment recommendations. Prior to further randomised controlled trials (RCTs) research is needed to understand a younger population in more detail.AimTo describe the baseline characteristics of patients with a meniscal tear and explore any association between baseline characteristics and outcome.MethodologyA prospective, national multicentre cohort study was performed recruiting patients aged 18 to 55 presenting to secondary care. MRI analysis of arthritis was performed using Whole Organ Magnetic Resonance Imaging Score (WORMS) and bone shape analysis. Outcomes included the Western Ontario Meniscal Evaluation Tool (WOMET) and Knee Injury and Osteoarthritis Outcome Score (KOOS4) at 12 months.Results150 participants were recruited across eight sites with a mean age of 43.47 (SD 9.63). MRI analysis using WORMS score and bone shape analysis revealed no or early osteoarthritis. At 12 months, 67 (44.67%) of participants were managed non-operatively and 68 (45.33%) were operatively. Participants in the operative group were significantly younger with a lower BMI (p<0.05). A stepwise logistic regression model including 17 characteristics revealed that only baseline score and surgery significantly affected 12-month WOMET and KOOS4.ConclusionThis study in contrast to previous trials demonstrated a benefit of surgery for patients with a meniscal tear. The METRO study demonstrates that it is feasible to recruit younger patients and a future RCT is required using the study population included in this cohort.
Tuberculosis detection using a low-loss and highly sensitive photonic crystal fiber technique in the terahertz regime
Authors: Taya Sofyan A. , Alhamss Dana N. , Almawgani Abdulkarem H. M. , Alzahrani Ahmad , Colak Ilhami , Patel Shobhit K. 
Published: August 2023

This research paper introduces a design and numerical investigation of a photonic crystal fiber (PCF) sensor with a hollow core. The sensor is specifically designed to detect Mycobacterium tuberculosis in the frequency range of 1–2 THz. The cladding region of the PCF sensor incorporates six rectangular air holes and an absorbing layer known as the perfectly matched layer (PML), which is utilized to examine various optical properties. Through a thorough investigation, our designed PCF sensor demonstrates enhanced sensitivity of 98.692%, 98.721%, 98.75%, and 98.764% for four different infected samples of tuberculosis at a frequency of 1.6 THz. The sensor exhibits minimal confinement loss and effective material loss. Furthermore, the numerical aperture and effective mode index of the proposed sensor are analyzed. An effective area of 346,550, 345,110, 343,710, and 343,020µm2 for the four different infected samples of tuberculosis is obtained. The fabrication methods employed for this sensor are mentioned. Overall, this PCF sensor can be promising for a wide range of chemical, gas, and biosensing applications.
Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2
Authors: Clairon Quentin , Prague Mélanie , Planas Delphine , Bruel Timothée , Hocqueloux Laurent , Prazuck Thierry , Schwartz Olivier , Thiébaut Rodolphe , Guedj Jérémie 
Published: August 2023

Because SARS-CoV-2 constantly mutates to escape from the immune response, there is a reduction of neutralizing capacity of antibodies initially targeting the historical strain against emerging Variants of Concern (VoC)s. That is why the measure of the protection conferred by vaccination cannot solely rely on the antibody levels, but also requires to measure their neutralization capacity. Here we used a mathematical model to follow the humoral response in 26 individuals that received up to three vaccination doses of Bnt162b2 vaccine, and for whom both anti-S IgG and neutralization capacity was measured longitudinally against all main VoCs. Our model could identify two independent mechanisms that led to a marked increase in measured humoral response over the successive vaccination doses. In addition to the already known increase in IgG levels after each dose, we identified that the neutralization capacity was significantly increased after the third vaccine administration against all VoCs, despite large inter-individual variability. Consequently, the model projects that the mean duration of detectable neutralizing capacity against non-Omicron VoC is between 348 days (Beta variant, 95% Prediction Intervals PI [307; 389]) and 587 days (Alpha variant, 95% PI [537; 636]). Despite the low neutralization levels after three doses, the mean duration of detectable neutralizing capacity against Omicron variants varies between 173 days (BA.5 variant, 95% PI [142; 200]) and 256 days (BA.1 variant, 95% PI [227; 286]). Our model shows the benefit of incorporating the neutralization capacity in the follow-up of patients to better inform on their level of protection against the different SARS-CoV-2 variants.
Trial registration: This clinical trial is registered with ClinicalTrials.gov, Trial IDs NCT04750720 and NCT05315583.
Sources Online: Eine nachhaltige Infrastruktur für digitale wissenschaftliche Texteditionen auf der Grundlage von TEI Publisher und IIIF
Authors: Kränzle Andreas , Ritter Gerold , Sieber Christian 
Published: August 2023

Zusammenfassung
Der Beitrag zeigt auf, wie in den letzten Jahren auf Initiative verschiedener Stakeholder eine selbsttragende, kollaborativ organisierte Infrastruktur für digitale wissenschaftliche Texteditionen aufgebaut wurde, die den Prinzipien von Standardisierung und Nachhaltigkeit verpflichtet ist. Eine wachsende Zahl von Institutionen und Projekten nutzt das Angebot, wie am Beispiel des Staatsarchivs des Kantons Zürich aufgezeigt wird. Thematisiert wird auch die Kostenfrage.