bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prioritization tool for cilia-associated genes and their in vivo resources unveils new avenues for ciliopathy research
Authors: Van Sciver Robert E. , Caspary Tamara 
Published: September 2024

ABSTRACT
Defects in ciliary signaling or mutations in proteins that localize to primary cilia lead to a class of human diseases known as ciliopathies. Approximately 10% of mammalian genes encode cilia-associated proteins, and a major gap in the cilia research field is knowing which genes to prioritize to study and finding the in vivo vertebrate mutant alleles and reagents available for their study. Here, we present a unified resource listing the cilia-associated human genes cross referenced to available mouse and zebrafish mutant alleles, and their associated phenotypes, as well as expression data in the kidney and functional data for vertebrate Hedgehog signaling. This resource empowers researchers to easily sort and filter genes based on their own expertise and priorities, cross reference with newly generated -omics datasets, and quickly find in vivo resources and phenotypes associated with a gene of interest.
Human walking biomechanics on sand substrates of varying foot sinking depth
Authors: Grant Barbara F. , Charles James P. , D'Août Kristiaan , Falkingham Peter L. , Bates Karl T. 
Published: September 2024

ABSTRACT
Our current understanding of human gait is mostly based on studies using hard, level surfaces in a laboratory environment. However, humans navigate a wide range of different substrates every day, which incur varied demands on stability and efficiency. Several studies have shown that when walking on natural compliant substrates there is an increase in energy expenditure. However, these studies report variable changes to other aspects of gait such as muscle activity. Discrepancies between studies exist even within substrate types (e.g. sand), which suggests that relatively ‘fine-scale’ differences in substrate properties exert quantifiable influences on gait mechanics. In this study, we compared human walking mechanics on a range of sand substrates that vary in overall foot sinking depth. We demonstrated that variation in the overall sinking depth in sand was associated with statistically significant changes in joint angles and spatiotemporal variables in human walking but exerted relatively little influence on pendular energy recovery and muscle activations. Significant correlated changes between gait metrics were frequently recovered, suggesting a degree of coupled or mechanistic interaction in their variation within and across substrates. However, only walking speed (and its associated spatiotemporal variables) correlated frequently with absolute foot sinkage depth within individual sand substrates, but not across them. This suggests that a causative relationship between walking speed and foot sinkage depth within individual sand substates is not coupled with systematic changes in joint kinematics and muscle activity in the same way as is observed across sand substrates.
On the rate-limiting dynamics of force development in muscle
Authors: van der Zee Tim J. , Wong Jeremy D. , Kuo Arthur D. 
Published: September 2024

ABSTRACT
Skeletal muscles produce forces relatively slowly compared with the action potentials that excite them. The dynamics of force production are governed by multiple processes, such as calcium activation, cycling of cross-bridges between myofilaments, and contraction against elastic tissues and the body. These processes have been included piecemeal in some muscle models, but not integrated to reveal which are the most rate limiting. We therefore examined their integrative contributions to force development in two conventional types of muscle models: Hill-type and cross-bridge. We found that no combination of these processes can self-consistently reproduce classic data such as twitch and tetanus. Rather, additional dynamics are needed following calcium activation and facilitating cross-bridge cycling, such as for cooperative myofilament interaction and reconfiguration. We provisionally lump such processes into a simple first-order model of ‘force facilitation dynamics’ that integrate into a cross-bridge-type muscle model. The proposed model self-consistently reproduces force development for a range of excitations including twitch and tetanus and electromyography-to-force curves. The model's step response reveals relatively small timing contributions of calcium activation (3%), cross-bridge cycling (3%) and contraction (27%) to overall force development of human quadriceps, with the remainder (67%) explained by force facilitation. The same set of model parameters predicts the change in force magnitude (gain) and timing (phase delay) as a function of excitatory firing rate, or as a function of cyclic contraction frequency. Although experiments are necessary to reveal the dynamics of muscle, integrative models are useful for identifying the main rate-limiting processes.
Lung mechanics in juvenile and adult Chelonoidis carbonarius
Authors: Oliveira Paulo Roberto Custodio de , Trevizan-Baú Pedro , Souza Ray Brasil Bueno de , Klein Wilfried 
Published: September 2024

ABSTRACT
Testudines possess a rigid shell that influences the mechanics of the respiratory system. We studied respiratory mechanics in the terrestrial red-footed tortoise Chelonoidis carbonarius (Cryptodira), comparing juvenile individuals with a less ossified and more flexible carapace with adults with a well-ossified rigid shell. Combined with these ontogenetic differences, we analyzed respiratory system mechanics with animals in a supine and a prone position, as well as in the isolated lungs, to evaluate the impact of the viscera on breathing mechanics. To do so, we used established protocols to measure pulmonary volume (i.e. resting, VLr; and maximum, VLm), static (Cstat) and dynamic (Cdyn) compliance, and the work of breathing (W). We observed that isolated lungs displayed increased VLr, VLm, Cstat and Cdyn and decreased W. Additionally, pulmonary volume, compliance and W were affected by evaluated position, such as a smaller VLr in a supine position. Cdyn and W showed a volume dependency while frequency had less influence on these variables. At similar levels of ventilation, juveniles showed a lower W than adults when standardized by body mass, but similar W when standardized by VLr. Clear ontogenetic changes could be observed in breathing mechanics between juvenile and adult C. carbonarius. While these differences might largely be explained by variation in shell ossification, other explanations such as differences in visceral proportions or developmental degree of the post-pulmonary septum should also be taken into account.
The effect of temperature and breathing pattern on the surface activity of ground squirrel pulmonary surfactant
Authors: Tejura Akash , Sun Mengxi , McCaig Lynda , Staples James , Veldhuizen Ruud 
Published: September 2024

ABSTRACT
This study investigates how hibernation affects the surface activity of pulmonary surfactant with respect to temperature and breathing pattern. Surfactant was isolated from a hibernating species, the 13-lined ground squirrel, and a homeotherm, the rabbit, and analysed for biophysical properties on a constrained sessile drop surfactometer. The results showed that surfactant from ground squirrels reduced surface tension better at low temperatures, including when mimicking episodic breathing, as compared with rabbit surfactant. In addition, low temperature adaptation was also observed using only the hydrophobic components of surfactant from ground squirrels. Overall, the data support the conclusion that ground squirrel surfactant has adapted to maintain surface activity during low temperature episodic breathing patterns, and that temperature adaptation is maintained with the hydrophobic components of the surfactant.
Results of a Prospective Randomized Multicenter Study Comparing Indocyanine Green (ICG) Fluorescence Combined with a Standard Tracer Versus ICG Alone for Sentinel Lymph Node Biopsy in Early Breast Cancer: The INFLUENCE Trial
Authors: Pitsinis Vassilis , Kanitkar Rahul , Vinci Alessio , Choong Wen Ling , Benson John 
Published: September 2024

Abstract
Background
For clinically node-negative early breast cancer patients, sentinel lymph node biopsy (SLNB) using dual localization with blue dye and radioisotope (RI) is currently standard of care. Documented disadvantages with these tracers have prompted exploration of alternative agents such as fluorescent indocyanine green (ICG), which demonstrates high detection rates combined with other tracers. Results of a randomized study evaluating ICG as a single tracer for SLN identification are presented.

Methods
Overall, 100 patients with unilateral, clinically node-negative, biopsy-proven invasive breast cancer (≤5 cm) scheduled for SLNB were recruited in two separate randomized cohorts, with 50 patients receiving ICG alone. Cohort 1 received ICG alone (n = 25) or combined with RI [Technetium99] (n = 25), while Cohort 2 received ICG alone (n = 25) or combined with blue dye (n = 25). The primary outcome was sensitivity for SLN identification.

Results
Among evaluable patients (n = 97), the overall SLN identification rate was 96.9% (ICG alone = 97.9%; ICG + RI = 100%; ICG + blue dye = 92%). Node positivity rates were 14.9% for ICG alone, 16% for ICG combined with RI, and 20% for ICG combined with blue dye. There were no significant differences (p < 0.05) in performance parameters, with ICG alone being non-inferior to tracer combinations for procedural node positivity rates when adjusted for specific factors.

Conclusion
These results support potential use of ICG as a sole tracer agent for routine SLNB, thereby avoiding disadvantages of RI and/or blue dye. The latter can be safely withheld as a co-tracer without compromising detection of positive nodes in primary surgical patients.
Modified Apexification Procedures in Immature Necrotic Permanent Teeth: A Case Report
Authors: Sebastian Nikita , Annapoorna BM 
Published: September 2024

Immature necrotic permanent teeth with a significant amount of coronal hard tissue loss are treated by apexification procedures. These procedures do not encourage further root maturation, predisposing the teeth to possible root fractures. The modified apexification procedure simulates regenerative endodontic procedures in encouraging root development in terms of increased dentine thickness contributing to improved resistance to fracture, while allowing the canal space to be used for core retention. This case report presents an immature tooth treated by the modified apexification procedure with an 18-month follow-up. CPD/Clinical Relevance: An alternative therapy in managing immature necrotic permanent teeth is of relevance to clinicians.
Multiple Gastrointestinal Immune-Related Adverse Events From Immune Checkpoint Inhibitor Therapy
Authors: Barlowe Trevor S. , Saxena-Beem Shruti , Ishizawar Rumey C. , Herfarth Hans , Moon Andrew M. 
Published: September 2024

INTRODUCTION:
We aimed to describe immune-related adverse events (irAEs) affecting multiple organs of the gastrointestinal system in patients who received immune checkpoint inhibitors.

METHODS:
Within a 2,843 patient retrospective cohort consisting of patients with cancer treated with immune checkpoint inhibitors, we used the Electronic Medical Record Search Engine, an information retrieval system, to search free text in the medical record to identify patients with multiple gastrointestinal irAEs.

RESULTS:
Thirteen patients developed multiple gastrointestinal irAEs (0.46%). The most common patterns of multisystem gastrointestinal irAE were colitis + pancreatitis and colitis + enteritis.

DISCUSSION:
Multisystem gastrointestinal irAEs are rare but warrant further characterization and attention.
Dynamics of gas exchange and heart rate signal entropy in standard cardiopulmonary exercise testing during critical periods of growth and development
Authors: Blanks Zachary , Brown Donald E. , Cooper Dan M. , Aizik Shlomit Radom , Bar‐Yoseph Ronen 
Published: September 2024

AbstractStandard cardiopulmonary exercise testing (CPET) produces a rich dataset but its current analysis is often limited to a few derived variables such as maximal or peak oxygen uptake (V̇O2). We tested whether breath‐by‐breath CPET data could be used to determine sample entropy (SampEn) in 81 healthy children and adolescents (age 7–18 years old, equal sex distribution). To overcome challenges of the relatively small time‐series CPET data size and its nonstationarity, we developed a Python algorithm for short‐duration physiological signals. Comparing pre‐ and post‐ventilatory threshold (VT1) CPET phases, we found: (1) SampEn decreased by 9.46% for V̇O2 and 5.01% for V̇CO2 (p < 0.05), in the younger, early‐pubertal participants; and (2) HR SampEn fell substantially by 70.8% in the younger and 77.5% in the older participants (p < 0.001). Across all ages, females exhibited greater HR SampEn than males during both pre‐ and post VT1 CPET phases by 14.10% and 23.79%, respectively, p < 0.01. In females, late‐pubertal had 17.6% lower HR SampEn compared to early‐pubertal participants (p < 0.05). Breath‐by‐breath gas exchange and HR data from CPET are amenable to SampEn analysis that leads to novel insight into physiological responses to work intensity, and sex and maturational effects.
Innovating Instrument Handover Techniques for Robotic Scrub Nurses
Authors: Scheppach Carl , Wagner Lars , Spinner Caroline , Jell Alissa , Wilhelm Dirk 
Published: September 2024

Abstract
A proposed solution to address increasing scarcity of operating room (OR) nurses is the deployment of robotic scrub nurses (RSNs). One of the primary responsibilities of these robots is the handover of surgical instruments to the surgeon. Despite this tasks’ apparent simplicity, it requires great precision and timing, while seamless execution is essential for the surgical workflow. This paper outlines the unique challenges of the instrument handover process between a RSN and a surgeon taking place during laparoscopic surgery. After customizing existing solutions from different domains to meet the specific needs of laparoscopic surgery, we introduced these solutions to medical professionals in a simulated OR scenario, and performed a utility analysis to identify the most suitable solutions.
Optical coherence tomography-guided laser osteotomy: toward improvement of ablation efficiency
Authors: Hamidi Arsham , Cattin Philippe C. , Canbaz Ferda 
Published: September 2024

Abstract
This study proposes an additional feature of optical coherence tomography (OCT) as a guidance system for laser surgery, aiming to enhance ablation efficiency during laser osteotomy. A long-range Bessel-like beam OCT system is integrated with an Er:YAG laser. The signal sensitivity of the OCT system is measured under various conditions encountered during laser osteotomy. The results demonstrate that the OCT sensitivity decreases from 87.53 dB to 79.54 dB and 68.93 dB in the presence of debris and water, respectively. These findings highlight the potential application signal sensitivity of OCT as a criterion for detecting the accumulation of water and debris, which could lead to a reduction in ablation efficiency during laser osteotomy using Er:YAG laser.
Deep Learning-based Artificial Intelligence in Audio based Analysis of Swallowing using Cervical Auscultation
Authors: Salloum Hazem , Graf Simone , Schilling Berit , Richter Lena , Jeleff-Wölfler Olivia , Feussner Hubertus , Ostler Daniel , Wilhelm Dirk , Fuchtmann Jonas 
Published: September 2024

Abstract
Swallowing problems (dysphagia) is associated with significant morbidity and mortality therefore diagnosis and treatment of dysphagia is important. Diagnostic tests include screening procedures, clinical swallowing examinations, and instrumental examination procedures. A non-invasive diagnostic option is auscultation of the swallowing act. However, there are different statements about the reliability and validity of the manual execution of this test. We developed a mobile hardware system to record cervical sounds using two microphones on the neck to acquire audio a data set. To generate ground truth data, fiberendoscopic swallow examinations were performed simultaneously to identify dysphagia. In order to diagnostically assess the swallowing sounds a spectrogram based classification pipeline was developed. In a first step this enabled us to identify different swallowing patterns in healthy individuals. With an accuracy of ~95%, we were able to reliably detect swallows within audio recordings, while the classification of types of swallow (dry, water, solid food) indicate the need for further improvements within the project ahead. In the future, we anticipate AI based analysis of auscultated swallowing sounds to detect swallowing disorders and aspirations.
Model to Simulate Brain Biopsies Using a Navigated Robotic Guiding System and a Bone Cutting Laser
Authors: Tu Ha Thanh , Luder Yann , Röthlisberger Michel , Schicker Martina , Morawska Marta , Cordier Dominik 
Published: September 2024

Abstract
Brain biopsies are necessary in cases of unclear lesions on imaging studies to establish a treatment plan based on the histologic diagnosis. A previous study investigated the potential of lasers to make brain biopsies less invasive, faster and safer. The study demonstrated that lasers can create highly precise burr holes which themselves can act as a sufficient guide for the biopsy needle. Furthermore, lasers can create tangential canals in the bone which allows to biopsy brain regions that are usually impossible or hazardous to access. Building upon the results of the previous study, further research and technological advancements were pursued. This includes a biopsy needle attachment for the robot, which will be used to simulate brain biopsies using CARLO© (Cold Ablation Robot-guided Laser Osteotome) with its Er:YAG laser and navigated robotic guiding system. The study utilizes five freshly frozen skulls, which are immobilized using a Mayfield clamp. Prior to conducting the experiment, the NeuroPlan© software is employed to plan the path and angle of the biopsies. To align the preexperimental CT with the skull, referencing points on the skull and its surface are registered using a pointer. A small skin incision is performed to reach the area of bone where the laser ablates the bone for the biopsy. Preliminary experimental results suggest that the combined use of laser ablation and a guidance device enables precise bone ablation and accurate needle guidance for biopsies. These initial results demonstrate the potential of integrating laser technology and robotics in neurosurgery, potentially enabling less invasive, faster and safer biopsies, ultimately leading to better patient outcomes.
A Novel End Effector for Telemanipulated Suturing in Robot-Assisted Laparoscopy
Authors: Kirst Alexander , Hellings-Kuß Anja , Hagmann Katharina , Dyck Michael , Schlenk Christopher , Klodmann Julian 
Published: September 2024

Abstract
Suturing is an integral part of surgery. Specialized instrumentation facilitates manual needle handling to support laparoscopic suturing tasks, e.g. uterine closure, in minimally invasive surgery. Current solutions for robotassisted laparoscopy lack the possibility to integrate these instruments, making them suitable only for conventional laparoscopic surgery. This paper introduces a novel end effector design actuating a conventional suturing instrument. The end effector is integrated into the DLR MiroSurge system to facilitate telemanipulated suturing. The mechanical properties of the end effector are characterized and its feasibility for use in robot-assisted laparoscopy is demonstrated.
Nullspace Control for Automatic Ultrasound Gel Supply
Authors: Osburg Jonas , Ernst Floris 
Published: September 2024

Abstract
Ultrasound gel is used as a coupling medium in ultrasound procedures, thereby ensuring the entry of sound waves into the body of the patient and providing ultrasound images of high quality. In this paper, we present an approach to automatically supply ultrasound gel during robot guided ultrasound examinations. For this purpose, we combine a simple mechanical design consisting of a gel tube and a push mechanism with a specialized control strategy exploiting the robotic nullspace of 7 DoF redundant manipulator. Functionality is demonstrated by robotic ultrasound scans on phantoms, with gel being automatically applied when needed.
A Laryngoscope with Shape Memory Actuation
Authors: Fischer Nikola , Ho Patty , Marzi Christian , Schuler Patrick , Mathis-Ullrich Franziska 
Published: September 2024

Abstract
Endotracheal intubation is a medical procedure to secure a patient’s airways, which can be challenging in emergency situations due to an individual’s anatomy. Intubation blades can benefit from an adjustable design with shape memory alloys. We present a novel blade design with two degrees of freedom, continuously transforming a straight into a curved blade. Our demonstrators reached mean angular deflections up to 16∘ without exceeding outer blade temperatures of 40∘C. Mean forces of almost 24N were applicable. This approach has the potential to reduce the complexity of intubation procedures and increase the success rate, especially in time-critical emergency situations.
In situ minimally invasive 3D printing for bone and cartilage regeneration - a scoping review
Authors: Maintz Michaela , Tomooka Yukiko , Eugster Manuela , Gerig Nicolas , Sharma Neha , Thieringer Florian M. , Rauter Georg 
Published: September 2024

Abstract
Advancements in personalized medicine, threedimensional (3D) printing, miniaturization, and robot-assisted surgery are driving innovation in tissue engineering. A novel approach, known as in situ printing, focuses on the direct deposition of materials at the surgical site. Using the in situ printing approach, bone and/or cartilage defects can be addressed with high precision. Furthermore, highly customized 3D printed tissue constructs or implants can be deposited directly inside the body. Currently, most applications of in situ printing are limited to areas near the skin or open surgeries. Even though a minimally invasive approach would bring clinical benefits, only a few research groups have focused on this field. In this scoping review, we provide an overview of the current state of in situ minimally invasive 3D printing technology for bone and cartilage regeneration and discuss its advantages and current challenges.
Adaptive Contrast Enhancement for Digital Radiographic Images using Image-to-Image Translation
Authors: Popp Ann-Kathrin , Schumacher Mona , Himstedt Marian 
Published: September 2024

Abstract
Digital radiography in medicine is a widely used imaging method for obtaining visual information about the inside of a body. To prepare the acquired raw image for diagnostic evaluation, the contrast must be adjusted depending on the examined part of the body and the reason of acquisition. The contrast enhancement of an image can be considered as a style transfer or an image-to-image translation which is an important field in deep learning. Based on common methods like the pix2pix network that only translate from one domain into one other, we propose a method (cc-pix2pix) for translating into multiple domains in one training. We provide additional information about the examination to the network for a specific contrast adjustment. Compared to the pix2pix network, the ccpix2pix reduces the mean squared error by a factor of six and achieves an improvement of approximately seven percentage points based on the histogram intersection of source and target images.