anthonyyazdaniml/gliner-biomed-curated-corpus huggingface dataset:
Phenotype-driven gene prioritization is fundamental to diagnosing rare genetic disorders. While traditional approaches rely on curated knowledge graphs with phenotype-gene relations, recent advancements in large language models (LLMs) promise a streamlined text-to-gene solution. In this study, we evaluated five LLMs, including two generative pre-trained transformers (GPT) series and three Llama2 series, assessing their performance across task completeness, gene prediction accuracy, and adherence to required output structures. We conducted experiments, exploring various combinations of models, prompts, phenotypic input types, and task difficulty levels. Our findings revealed that the best-performed LLM, GPT-4, achieved an average accuracy of 17.0% in identifying diagnosed genes within the top 50 predictions, which still falls behind traditional tools. However, accuracy increased with the model size. Consistent results were observed over time, as shown in the dataset curated after 2023. Advanced techniques such as retrieval-augmented generation (RAG) and few-shot learning did not improve the accuracy. Sophisticated prompts were more likely to enhance task completeness, especially in smaller models. Conversely, complicated prompts tended to decrease output structure compliance rate. LLMs also achieved better-than-random prediction accuracy with free-text input, though performance was slightly lower than with standardized concept input. Bias analysis showed that highly cited genes, such as BRCA1, TP53, and PTEN, are more likely to be predicted. Our study provides valuable insights into integrating LLMs with genomic analysis, contributing to the ongoing discussion on their utilization in clinical workflows.
Decreased left atrial appendage velocity (LAAV) is considered a significant risk factor thrombus formation in the left atrial appendage (LAA). The aim of this study was to assess the role of echocardiographic left atrial (LA) function parameters in predicting LAAV in patients with persistent atrial fibrillation (AF) undergoing catheter ablation. We prospectively enrolled consecutive patients with persistent AF undergoing transesophageal echocardiography (TEE) directly before the first AF ablation in 2019-2022. Of the 150 patients enrolled in the study, 29.3% (n = 44) had reduced LAAV values defined as < 25 cm/s. Patients with decreased LAAV values exhibited significantly reduced left atrial reservoir and conduit strain (LASr and LAScd), LA emptying fraction, and average e' values. This group also presented with a high LA stiffness index (LASI), high LA and right atrial area, and high LA volume index (LAVI) and E/e' ratio. In multivariable logistic regression analysis, LASI and LAVI remained significant predictors of the reduced LAAV. The threshold values were 1.6 for LASI and 44.47 ml/m2 for LAVI, with area under the curve values of 0.809 and 0.755, respectively. Among all noninvasive echocardiographic parameters, LASI and LAVI were found to be the best predictors of reduced LAAV, with good sensitivity and specificity. Moreover, LASI was found to be the only significant predictor of reduced LAAV defined as < 20 cm/s as well as < 25 cm/s.
As people walk and interact with objects such as when opening a door, their movements make sounds. It is possible that these sounds are also used as feedback to stabilize and adapt movement. There is some evidence for such a connection between the auditory and motor systems in activities of daily living, yet the empirical work is insufficient because the role of the auditory system in movement is a relatively neglected topic. The objective of this study is to address this gap. The study will also evaluate the potential for improvements in movement stability and variability by restricting or augmenting the auditory feedback from the participants' footstep sounds. Eligibility is based on inclusion and exclusion criteria determined via a self-report questionnaire. The inclusion criteria are age and overall health status (young healthy adults, 19-35) and self-reported ability to walk comfortably for half an hour. Exclusion criteria include known hearing impairment, history of back or lower extremity injury, surgery that affects mobility, neurological disease or impairment that limits the ability to walk (Cerebral palsy). The study will randomly split the participants in a control and experimental group. Participants will perform trials in one condition only, quiet walking or control. Participants will visit the lab five times in the span of two weeks. The first and last sessions will serve for pre-post comparisons.
Insomnia is a common health problem. Untreated insomnia may lead to decreased physical and mental health. The patients turns to Primary Health Care when daytime symptoms decrease social and occupational function. Previous studies have shown that cognitive and behavioral therapy have effects on insomnia and recommends as first line treatment but is not widely available in primary health care.

The purpose is to test the effect of group intervention in Primary Health Care for patients with insomnia. The outcomes is insomnia severity, sleep habits, use of hypnotics, Fatigue, general health and health related quality of life. Characters with insomnia visiting in Primary Health Care.
All intubated patients cared for by the Medical Intensive Care Unit (MICU)team during the study period will be evaluated. After 24 hours of mechanical ventilation, patients not meeting any exclusionary criteria will be considered for entrance into our trial. We will attempt to obtain consent as soon as the 24 hour period is fulfilled, even if the patient is not ready for extubation at that point. This is to maximize the success rate for obtaining consent without delaying the SBT when the patient is clinically ready. Given the nature of this protocol, we expect that the informed consent will primarily be obtained from the patient's family member or POA. For all patients who regain competency, they will be re-consented for permission to use their data that has been collected.

Once patients are consented, they will be followed daily by the study investigators. When the order is written by the MICU team for the patient to undergo a SBT, the patient's level of consciousness will be evaluated by the nursing staff using the RASS. If the patient's score is \<(-2), they will notify the study investigators. The patient will then be randomized by sealed envelope to one of two study groups. Group 1 will immediately undergo their SBT while still sedated. Group 2 will have their sedation held. Once their RASS score is 0 or higher and they can follow simple commands (holding up two fingers to command), they will be initiated on their SBT.

The standard duration of an SBT by protocol is 2 hours. The duration of SBT may be shorter at the discretion of the ICU attending physician. Additionally, the standard ventilators settings for an SBT is 10 cm of Pressure Support and 5 cm of PEEP (positive and expiratory pressure). This may vary some by the attending's preference though we encourage the use of the standard setting during the study unless there is a clear need to deviate from the protocol. This is to limit the confounding impact that differing levels of Pressure Support may have on the parameters tracked. Patients who are felt to be failing the SBt will be placed back on fill ventilator support at any point directed by the MICU team. Given the lack of objective criteria to define failure of SBT, there are no clear criteria defined and the decision that a patient is failing their SBT will be determined by the attending physician.

Nursing staff will be provided with a documentation form (Data sheet 1) and asked to annotate heart rate, blood pressure, respiratory rate, tidal volume, oxygen saturation, and RASS score at 0, 15, 30, 60 minutes and at the conclusion of the SBT.They will be inserviced on the protocol prior to the start of the study. The study investigators will collect demographic information and record it on Data sheet 2. In addition to the primary endpoint(changes in cardiopulmonary parameters and RASS collected by the nursing staff), secondary endpoints will include outcome of first SBT(pass or fail), time from randomization to extubation, outcome of the first extubation (Data sheet 1). As stated earlier, there are no clearly defined cut-off values for any of the monitored variables that define failure of an SBT.
Osteoarthritis (OA) is the most common musculoskeletal condition affecting the quality of life of older adults. The prevalence of OA is very high 45% in females in comparison to males, especially after menopause due to the hormonal changes. In the physical therapy practice, therapeutic ultrasound (US) is one of the most frequently applied electrotherapeutic modalities in orthopedics physiotherapy. Simultaneous application of two therapeutic modalities at the same site is described as combination therapy (CT). The most commonly used CT is US \& Transcutaneous neuromuscular electrical stimulation (TENS )where this approach was effective in pain modulation .The use of combination therapy is highly preferable because of the advantageous effect both electro-therapy and ultrasound provide simultaneously. There are no current studies on using combination therapy in the treatment of pain in mild to moderate knee osteoarthritis in post-menopausal women and we don't know the proper treatment dose.The study is designed as a prospective, randomized, pre-posttest, controlled trial.where we have two groups Intervention group and control. the intervention group will recieve strengthening exercises in addition to combination therapy 10 minutes for each session, 3 times per week, for 3 weeks.The Control group will recieve the same strengthening exercises as intervention group and sham combination therapy 10 minutes for each session, 3 times per week, for 2 weeks.
PCT No. PCT/US96/04215 Sec. 371 Date Sep. 19, 1997 Sec. 102(e) Date Sep. 19, 1997 PCT Filed Mar. 27, 1996 PCT Pub. No. WO96/30377 PCT Pub. Date Oct. 3, 1996Novel macrocyclic compounds are constructed to include large cyclic structures that are interrupted by at least one ring system. Each interrupting ring system includes two bridgehead atoms. Bridgehead atoms are bonded to one or more bridges that interconnect one or more ring systems thereby forming a large cyclic structure. Located in each bridge are two or more nitrogenous moieties that are derivatized with chemical functional groups. The ring systems can include further nitrogenous moieties, either as ring atoms or on pendant groups attached to the ring. These can also be derivatized with chemical functional groups. The totality of the chemical functional groups imparts certain conformational and other properties to the macrocyclic compounds. In accordance with certain embodiments of the invention, libraries of such macrocyclic compounds are prepared utilizing permutations and combinations of the chemical functional groups and the nitrogenous moieties to build complexity into the library.
The present invention relates to a medicine for treating alopecia areata, which is a traditional Chinese medicine preparation of oral administration. The present invention is characterized in that dose for one day is made from the following traditional Chinese medicine raw material of 12 grams of pinellia tubers, 8 grams of fleece-flower roots, 8 grams of arborvitae seeds, 10 grams of Chicken's gizzard membranes (fried and ground), 7 grams of prepared rhizomes of rehmannia, 10 grams of tuckahoe, 10 grams of pilose asiabell roots, 10 grams of astragalus roots and 8 grams of Chinese caterpillar fungi. The present invention has the efficiency of liver and kidney nourishing, qi and blood nourishing, meridian dredging, blood circulation promotion, wind dispelling, itch arrest, hair solidification and hair restoration without side effect. The present invention has the advantages of convenient administration and rapid effect taking. New hair grows out at alopecia areata points in one month, the alopecia areata is generally cured after two to five treatment courses, and the therapeutic effect is significant. The clinic tracking of 200 people shows that he therapeutic rate is 95%. The present invention is suitable for various alopecia and alopecia areata pathological symptoms.
PURPOSE: Despite standardized biomechanical tests for spinal implants, we recently recognized pedicle screw failure to maintain the rod fixated as a clinical concern in scoliosis surgery. This occurrence study investigates the risk and magnitude of axial rod slip (ARS), its relation with technique and preventive measures.
METHODS: Retrospective multicenter review of all primary scoliosis cases (2018-2020) with > 1 year FU from three centers, instrumented with uniplanar screws and 5.5 mm CoCr rods (Mesa 2, Stryker Corporation, Kalamazoo, MI, USA). ARS was defined as > 1 mm change in residual distal rod length from the screw in the lowest instrumented vertebra (LIV) and assessed by two independent observers. Slip distance, direction, relation to distal screw density and time of observation were recorded, as well as the effect of ARS on caudal curve increase. To prevent slip, more recent patients were instrumented with a different end-of-construct screw (Reline, NuVasive Inc. San Diego, CA, USA) and analyzed for comparison.
RESULTS: ARS risk was 27% (56/205) with a distance of 3.6 ± 2.2 mm, predominantly convex. 42% occurred before 4 months, the rest before 1 year. The caudal curve substantially increased three times more often in patients with ARS. Interobserver reliability was high and slip was in the expected direction. ARS was unrelated to distal screw density. Remarkable variation in ARS rates (53%, 31%, 13%) existed between the centers, while there was no difference in mean screw density (≈1.3 screws/level) or curve correction (≈60%). Revision surgery for ARS was required in 2.9% (6/207). Using the different end-of-construct screw, ARS risk was only 2% (1/56) and no revisions were required.
CONCLUSION: This study demonstrates the prevalence of axial rod slip at the end of construct in scoliosis surgery and its clinical relevance. While minimal ARS can be subclinical, ARS should not be mistaken for adding on. The most severe ARS predominantly occurred convex at the high-loaded distal screw when L3 was the LIV. Longer constructs (LIV L3 or L4) have a higher risk of ARS. The minimal risk of ARS with another end-of-construct screw underscores the influence of screw type on ARS occurrence in our series. Further research is essential to refine techniques and enhance patient outcomes.
SARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK's national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14-180 days after receiving their most recent vaccination had a lower risk of reinfection than those >180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30-45 years, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection.
A method and system for mucosally administering a macromolecular drug to the mucosa of the oral cavity is shown. The system comprises an inner drug/enhancer/polymer layer (11) having one surface adapted to contact and adhere to the mucosal tissue of the oral cavity and an opposing surface in contact with and adhering to an overlying inert layer (12). The inner layer (11) contains from about two to sixty percent by weight of a bile salt enhancer, five to sixty five percent by weight of a hydrophilic polymer which is water soluble or swellable and an effective amount of a macromolecular drug having a molecular weight of at least 500 daltons. Polysaccharides, polypeptides and proteins are preferred forms of macromolecular drugs. The bile salt enhancer facilitates the delivery of macromolecules such as low molecular weight heparin and calcitonin. The polymer serves as a plasticizer to prevent the crystallization and/or aggregation of such macromolecular drugs. Hydroxypropyl cellulose is a particularly suitable polymer.
Clofarabine Injection is supplied in single-dose flint vials containing 20 mg of clofarabine in 20 mL of solution. Each box contains one Clofarabine Injection vial (NDC 72266-108-01). The 20 mL flint vials contain 20 mL (20 mg) of solution. The pH range of the solution is 4.5 to 7.5.

Vials containing undiluted Clofarabine Injection should be stored at 25°C (77°F); excursions permitted to 15 - 30°C (59 - 86°F).

Diluted admixtures may be stored at room temperature, but must be used within 24 hours of preparation.

Procedures for proper handling and disposal should be utilized. Handling and disposal of Clofarabine Injection should conform to guidelines issued for cytotoxic drugs. Several guidelines on this subject have been published. 1
Although collagen can be used as a medical material, its use for humans has a risk of allergy and zoonosis. Here, the use of artificial collagen or the like as a medical material is under investigation. However, the conventional artificial collagen is not necessarily perfect in terms of physical strength, denaturation upon heating, and inability to be processed into a sheet form, and thus, the practical invention is still insufficient. The present invention prepares a polymer peptide by oxidatively crosslinking a collagen mimetic peptide having a triple helix structure composed of 3 peptide chains containing a plurality of cysteine (Cys) residues. The present polymeric peptide can be processed into a hydrogel or a film sheet, and can impart a specific physiological function such as cell adhesion by integrating a functional amino acid sequence present in a biopolymer. Further, the present invention provides a method for producing the above-mentioned polymeric peptide and the like, and provides uses as a composition for cell culture, wound coating, regenerative medical materials, research materials and the like, in which these polymeric peptide and gel have been used.
Risk Summary

Based on findings from animal studies and its mechanism of action, IMFINZI can cause fetal harm when administered to a pregnant woman [see Clinical Pharmacology (12.1)]. There are no available data on the use of IMFINZI in pregnant women.

In animal reproduction studies, administration of durvalumab to pregnant cynomolgus monkeys from the confirmation of pregnancy through delivery at exposure levels approximately 6 to 20 times higher than those observed at the clinical dose of 10 mg/kg based on area under the curve (AUC), resulted in an increase in premature delivery, fetal loss, and premature neonatal death (see Data). Human immunoglobulin G1 (IgG1) is known to cross the placental barrier; therefore, durvalumab has the potential to be transmitted from the mother to the developing fetus. Apprise pregnant women of the potential risk to a fetus.

In the U.S. general population, the estimated background risk of major birth defects and miscarriage in clinically recognized pregnancies is 2 to 4% and 15 to 20%, respectively.

Data

Animal Data

As reported in the literature, the PD-1/PD-L1 pathway plays a central role in preserving pregnancy by maintaining maternal immune tolerance to the fetus. In mouse allogeneic pregnancy models, disruption of PD-L1 signaling was shown to result in an increase in fetal loss. The effects of durvalumab on prenatal and postnatal development were evaluated in reproduction studies in cynomolgus monkeys. Durvalumab was administered from the confirmation of pregnancy through delivery at exposure levels approximately 6 to 20 times higher than those observed at a clinical dose of 10 mg/kg (based on AUC). Administration of durvalumab resulted in premature delivery, fetal loss (abortion and stillbirth), and increase in neonatal deaths. Durvalumab was detected in infant serum on postpartum Day 1, indicating the presence of placental transfer of durvalumab. Based on its mechanism of action, fetal exposure to durvalumab may increase the risk of developing immune-mediated disorders or altering the normal immune response and immune-mediated disorders have been reported in PD-1 knockout mice.
Citicoline eye drops 2%. One drop in the study eye three times daily throughout the 3-year trial. Patients will be treated with any IOP-lowering agent to control IOP and study treatments should be administered at least 20 minutes after IOP lowering medication.
Clinical use of gene panel testing for hematopoietic neoplasms in areas, such as diagnosis, prognosis prediction, and exploration of treatment options, has increased in recent years. The keys to interpreting gene variants detected in gene panel testing are to distinguish between germline and somatic variants and accurately determine whether the detected variants are pathogenic. If a variant is suspected to be a pathogenic germline variant, it is essential to confirm its consistency with the disease phenotype and gather a thorough family history. Donor eligibility must also be considered, especially if the patient's variant is also detected in the expected donor for hematopoietic stem cell transplantation. However, determining the pathogenicity of gene variants is often complicated, given the current limited availability of databases covering germline variants of hematopoietic neoplasms. This means that hematologists will frequently need to interpret gene variants themselves. Here, we outline how to assess the pathogenicity of germline variants according to criteria from the American College of Medical Genetics and Genomics/Association for Molecular Pathology standards and guidelines for the interpretation of variants using DDX41, a gene recently shown to be closely associated with myeloid neoplasms with a germline predisposition, as an example.
BACKGROUND: Febrile seizures (FSs) are the most common form of epilepsy in children aged between six months and five years. The exact cause is unknown, but several studies have demonstrated the importance of genetic predisposition, with increasing involvement of receptors and ion channels. The present study aims to identify novel pathogenic variants in Italian patients with FSs.
METHODS: We performed targeted panel sequencing in a cohort of 21 patients with FSs. In silico analysis was performed to predict the pathogenic role of the resulting variants.
RESULTS: We found two novel variants segregating in two families with FSs: c.1021C>G (p.Leu341Val) in the CHRNA2 gene and c.140A>G (p.Glu47Gly) in SCN2A.
CONCLUSIONS: The c.1021C>G (p.Leu341Val) variant leads to a codon change of highly conserved leucine to valine at position 341 and is located in segments M3 of the subunit, which is important for channel gating. The c.140A>G (p.Glu47Gly) variant causes a substitution of glutamic acid with glycine at position 47 of the protein, which is highly conserved across the species. Moreover, it is located in the N-terminal domain, a region commonly affected in ASD, which impacts the inactivation kinetics and voltage dependence of steady-state activation. Further analyses are needed to better explain the role of CHRNA2 and SCN2A in the development of febrile seizures.