gebhart/patrepeval huggingface dataset:
Inhibition of miR-92a Enhances Fracture Healing via Promoting Angiogenesis in a Model of Stabilized Fracture in Young Mice (2013)

MicroRNAs (miRNAs) are endogenous small noncoding RNAs regulating the activities of target mRNAs and cellular processes. Although no miRNA has been reported to play an important role in the regulation of fracture healing, several miRNAs control key elements in tissue repair processes such as inflammation, hypoxia response, angiogenesis, stem cell differentiation, osteogenesis, and chondrogenesis. We compared the plasma concentrations of 134 miRNAs in 4 patients with trochanteric fractures and 4 healthy controls (HCs), and the levels of six miRNAs were dysregulated. Among these miRNAs, miR-92a levels were significantly decreased 24 hours after fracture, compared to HCs. In patients with a trochanteric fracture or a lumbar compression fracture, the plasma concentrations of miR-92a were lower on days 7 and 14, but had recovered on day 21 after the surgery or injury. To determine whether systemic downregulation of miR-92a can modulate fracture healing, we administered antimir-92a, designed using locked nucleic acid technology to inhibit miR-92a, to mice with a femoral fracture. Systemic administration of antimir-92a twice a week increased the callus volume and enhanced fracture healing. Enhancement of fracture healing was also observed after local administration of antimir-92a. Neovascularization was increased in mice treated with antimir-92a. These results suggest that plasma miR-92a plays a crucial role in bone fracture healing in human and that inhibition of miR-92a enhances fracture healing through angiogenesis and has therapeutic potential for bone repair.
5,5′-Dimethyl-4,4′-bis[2-(2-methyl-3-thienyl)cyclopentenyl]-2,2′-bithiophene (2007)

The molecule of the title compound, C30H30S4, is located on a centre of inversion. The cyclopentene ring is almost planar. The thio­phene rings are twisted out of the plane of the cyclo­pentene ring by 47.41 (8) and 46.25 (9)°.
Eye Movements in Response to Electrical Stimulation of the Lateral and Superior Ampullary Nerves (2011)

It is possible to stimulate electrically the lateral and superior ampullary nerves without simultaneous stimulation of the facial nerve. Because the nerves run close to each other, electrical stimulation provoked eye movements that were not purely horizontal, but also had some vertical components. Nevertheless, this site can be used to encode horizontal movements, because central adaptation may correct unnatural afferent vestibular cues delivered by a prosthetic sensor. The range of stimulus intensities that produced a response was broad enough for us to envision the possibility of encoding eye movements of various speeds.
Combining homolog and motif similarity data with Gene Ontology relationships for protein function prediction (2012)

Uncharacterized proteins pose a challenge not just to functional genomics, but also to biology in general. The knowledge of biochemical functions of such proteins is very critical for designing efficient therapeutic techniques. The bottleneck in hypothetical proteins annotation is the difficulty in collecting and aggregating enough biological information about the protein itself. In this paper, we propose and evaluate a protein annotation technique that aggregates different biological information conserved across many hypothetical proteins. To enhance the performance and to increase the prediction accuracy, we incorporate term specific relationships based on Gene Ontology (GO). Our method combines PPI (Protein Protein Interactions) data, protein motifs information, protein sequence similarity and protein homology data, with a context similarity measure based on Gene Ontology, to accurately infer functional information for unannotated proteins. We apply our method on Saccharomyces Cerevisiae species proteins. The aggregation of different sources of evidence with GO relationships increases the precision and accuracy of prediction compared to other methods reported in literature. We predicted with a precision and accuracy of 100% for more than half proteins of the input set and with an overall 81.35% precision and 80.04% accuracy.
A theoretical and experimental study of non-linear absorption properties of substituted 2,5-di-(phenylethynyl)thiophenes and structurally related compounds (2009)

Photo-physical properties relevant for optical power limiting in the near-visible and visible regions of the spectrum are reported for a series of substituted diarylalkynyl chalcogenophenes (furans, thiophenes, selenophenes, and tellurophenes). The linear ground and excited state absorption as well as the nonlinear (two-photon) absorption were determined at the time-dependent density functional theory level with use of the hybrid exchange-correlation functionals B3LYP and CAM-B3LYP. A selected number of the theoretically studied molecules were synthesized and characterized experimentally with the use of absorption and luminescence spectroscopy. The photo-physical data are compared to the results from optical power limiting measurements performed in THF solution at a wavelength of 532 nm, with a laser pulse length of 5 ns and pulse energies up to 150 µJ. The best compounds in the present investigation display an energy damping by approximately a factor of 10 at a concentration of 0.010 M.
Experimental tests of a new correlated chromophore domain model of self-healing in a dye-doped polymer (2013)

Temperature-dependent photodegradation and recovery studies of Dipserse Orange 11 (DO11) dye dissolved in poly(methyl methacrylate) and polystyrene polymer hosts are used as a test of a new model that builds on the recently proposed correlated chromophore domain model. [Ramini and Kuzyk, J. Chem. Phys., 2012, 137, 054705.] Our model posits that dye molecules form domains or aggregates. The nature of aggregation or how it mediates self-healing is not yet well understood. In this paper we present evidence that supports the hypothesis that the dye molecules undergo a change to a state with higher dipole moment whether it be a tautomer or a TICT state and hydrogen bond with the amines and keto-oxygens of the polymer. Groupings of such molecules in a polymer chain form what we call a domain, and interactions between molecules in a domain make them more robust to photodegradation and mediate self-healing. All of the data is found to be consistent with our new model in the time–temperature–intensity–concentration domain.
Fecal microbiota transplantation as novel therapy in gastroenterology: A systematic review (2015)

FMT is highly effective in CDI, and holds promise in UC. As for CD, chronic constipation, pouchitis and IBS data are too limited to draw conclusions. FMT increases insulin sensitivity in metabolic syndrome.
Evaluation of a Framework for Case Development and Simulated Patient Training for Complex Procedures (2006)

Actors can be trained to portray patients undergoing complex procedures. Our framework for case development and SP training was effective in creating realistic roles. Future studies could evaluate this framework for additional procedures.
Robust modem and coding techniques for FM hybrid ICOC DAB (1997)

The design of robust modem and FEC (forward error correction) code techniques with application to the transmission of an FM hybrid analog/digital in-band on-channel (IBOC) digital audio broadcast (DAB) signal is presented here. The FEC codes are derived from an original lower rate convolutional code (R=1/3). The original code is segmented into a pair of "complementary" components, which form independent codes, each with a higher rate (less redundancy) than the base code. The exploitation of channel state information (CSI) and special interleaving techniques are described for application to FM hybrid IBOC DAB with its unique interference environment and selective fading due to multipath. Simulation results confirm the robustness of the design.
A Case of Panhypopituitarism and Central Diabetes Insipidus Caused by Primary Central Nervous System Lymphoma (2008)

Primary central nervous system (CNS) lymphoma is an uncommon neoplasm. However, the incidence of primary CNS lymphoma has increased more than 10-fold over the past three decades, and continues to accelerate. Currently, primary CNS lymphoma represents 4 to 7 percent of all newly diagnosed primary CNS tumors. Primary CNS lymphoma may arise from different parts of the brain, with deep hemispheric periventricular white matter being the most common site of origin. The presenting symptoms in primary CNS lymphoma vary depending on the location of the mass. Involvement of the hypothalamic-pituitary axis may cause hypopituitarism, diabetes insipidus, headache, diplopia, and blurred vision.
Monolithic Injection-Locked High-Speed Semiconductor Ring Lasers (2008)

We propose a monolithic optically injection-locked laser system on one chip, without the use of an isolator. This system is based on the availability of two modes in a ring laser (clockwise, and counter-clockwise). In a ring laser whose operation is dominated by the counter-clockwise mode, the clockwise mode power is significantly reduced. Hence, the coupling between the master laser and the ring laser is highly unidirectional, due to the direction of the ring laser output. This monolithic injection locking system is predicted to exhibit a greatly enhanced resonance frequency and modulation bandwidth under ultrahigh injection locking conditions.
Coil Retrieval following Embolization of Cerebral Aneurysms (2003)

Failed coil embolization of cerebral aneurysms may be occasionally followed by direct surgical treatment. We had 5 patients who underwent coil retrieval and surgical clipping after coil embolization because of periprocedural complications. The patients, ranging in age from 40 to 71, had wide-neck aneurysms located at the anterior communicating artery (AcomA) in 3 patients, the middle cerebral artery (MCA) in 1, and the internal carotidophthalmic artery (IC-Ophthalmic) in 1. They were embolized with Guglielmi detachable coils (GDCs), which had to be retrieved within 8 days because of coil protrusion and migration in 3 patients, aneurysm rupture in 1, and increased mass effect due to coil compaction in 1. Coils were successfully removed with aneurysmotomy or arteriotomy under temporary trapping, aneurysms were then clipped or trapped. Three patients had a good outcome, but one suffered permanent visual disturbance and the other had a motor deficit. Our study revealed that a small AcomA aneurysm had a high risk of complication in a case of complex anatomy of the AcomA-A1-A2 complex with its difficult access. In addition, insufficient packing of the inflow zone in a large and symptomatic aneurysm may cause coil compaction and regrow with increasing mass effect. The indication and treatment strategy for these aneurysms should be carefully determined.
Medical Instructed Real-Time Assistant for Patient with Glaucoma and Diabetic Conditions (2020)

Virtual assistants are involved in the daily activities of humans such as managing calendars, making appointments, and providing wake-up calls. They provide a conversational service to customers around-the-clock and make their daily life manageable. With this emerging trend, many well-known companies launched their own virtual assistants that manage the daily routine activities of customers. In the healthcare sector, virtual medical assistants also provide a list of relevant diseases linked to a specific symptom. Due to low accuracy and uncertainty, these generated recommendations are untrusted and may lead to hypochondriasis. In this study, we proposed a Medical Instructed Real-time Assistant (MIRA) that listens to the user’s chief complaint and predicts a specific disease. Instead of informing about the medical condition, the user is referred to a nearby appropriate medical specialist. We designed an architecture for MIRA that considers the limitations of existing virtual medical assistants such as weak authentication, lack of understanding multiple intent statements about a specific medical condition, and uncertain diagnosis recommendations. To implement the designed architecture, we collected the chief complaints along with the dialogue corpora of real patients. Then, we manually validated these data under the supervision of medical specialists. We then used these data for natural language understanding, disease identification, and appropriate response generation. For the prototype version of MIRA, we considered the cases of glaucoma (eye disease) and diabetes (an autoimmune disease) only. The performance measure of MIRA was evaluated in terms of accuracy (89%), precision (90%), sensitivity (89.8%), specificity (94.9%), and F-measure (89.8%). The task completion was calculated using Cohen’s Kappa ( k = 0.848 ) that categorizes MIRA as ‘Almost Perfect’. Furthermore, the voice-based authentication identifies the user effectively and prevent against masquerading attack. Simultaneously, the user experience shows relatively good results in all aspects based on the User Experience Questionnaire (UEQ) benchmark data. The experimental results show that MIRA efficiently predicts a disease based on chief complaints and supports the user in decision making.
GA4GH: International policies and standards for data sharing across genomic research and healthcare (2021)

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
Just Undercompensation: The Idiosyncratic Premium n Eminent Domain (2013)

a state court, even if it be authorized by statute, whereby private property
O38 PROPHYLACTIC LIQUID MESH - A SMALL ANIMAL EXPERIMENT (2021)

Abstract Aim Background: Surgical mesh is widely used not only to treat but also to prevent incisional hernia formation. Despite much effort by material engineers, the ‘ideal' mesh mechanically, biologically and surgically easy to use remains elusive. Advances in tissue engineering and nanomedicine have allowed new concepts to be tested with promising results in both small and large animals. Abandoning the concept of a pre-formed mesh completely for a ‘pour in liquid mesh’ has never been tested before. Material and Methods Thirty rabbits underwent midline laparotomy with closure using an absorbable suture and small stitch small bites technique. In addition, their abdominal wall closure was reinforced by a liquid nanofibrous scaffold composed of a fibrin sealant and nanofibers of poly-ε-caprolactone with or without hyaluronic acid or the sealant alone, placed as an ‘onlay’ over the closed abdominal wall. The animals were sacrificed at 6 weeks and their abdominal wall was subjected to histological and biomechanical evaluations. Results All the animals survived the study period with no major complication. Histological evaluation showed an eosinophilic infiltration in all groups and foreign body reaction more pronounced in the groups with nanofibers. Biomechanical testing demonstrated that groups treated with nanofibers developed a scar with higher tensile ultimate and yield strength. Conclusions The use of nanofibers in a liquid form applied to the closed abdominal wall is easy to use and improves the biomechanical properties of healing fascia at 6 weeks after midline laparotomy in a rabbit model.
Fermionic Orbital Optimization in Tensor Network States (2016)

Tensor network states and specifically matrix-product states have proven to be a powerful tool for simulating ground states of strongly correlated spin models. Recently, they have also been applied to interacting fermionic problems, specifically in the context of quantum chemistry. A new freedom arising in such nonlocal fermionic systems is the choice of orbitals, it being far from clear what choice of fermionic orbitals to make. In this Letter, we propose a way to overcome this challenge. We suggest a method intertwining the optimization over matrix product states with suitable fermionic Gaussian mode transformations. The described algorithm generalizes basis changes in the spirit of the Hartree-Fock method to matrix-product states, and provides a black box tool for basis optimization in tensor network methods.
Location of ChlorophyllZ in Photosystem II (1994)

Saturation-recovery and progressive microwave power saturation EPR spectroscopies have been used to probe the location of the chlorophyllZ+ (ChlZ+) radical species in Mn-depleted photosystems II (PSII). The spin-lattice relaxation transients of ChlZ+ were non-single-exponential due to a dipole-dipole interaction with one of the other paramagnetic centers in PSII. Measurements on CN(-)-treated, Mn-depleted PSII membrane samples, in which the non-heme Fe(II) is converted into its low-spin, diamagnetic form, confirmed that the non-heme Fe(II) caused the dipolar relaxation enhancement of ChlZ+. The saturation-recovery EPR data were fit to a dipolar model [Hirsh, D. J., Beck, W. F., Innes, J. B., & Brudvig, G. W. (1992) Biochemistry 31, 532] which takes into account the isotropic (scalar) and orientation-dependent (dipolar) contributions to the spin-lattice relaxation of the radical. The temperature dependence of the dipolar rate constants of ChlZ+ was identical to the temperature dependencies recently observed for the stable tyrosine radical, YD., and the special pair bacteriochlorophyll radical, (BChla)2+, in PSII and in reaction centers from Rhodobacter sphaeroides, respectively. Because the non-heme Fe(II) is known to cause a dipolar relaxation enhancement of the radicals in both of the latter cases, this result provides further evidence that the non-heme Fe(II) causes the dipolar relaxation enhancement of ChlZ+ and, moreover, demonstrates that the magnetic properties of the non-heme Fe(II) in PSII and in reaction centers from Rhodobacter sphaeroides are very similar. By using the known Fe(II)-(BChla)2+ distance for calibration, we estimate the Fe(II)-ChlZ+ distance to be 39.5 +/- 2.5 A.(ABSTRACT TRUNCATED AT 250 WORDS)
Comparison of ethylene oxide and propylene oxide chemisorbed on clean and oxygen precovered Ag(110) (1992)

The adsorption of ethylene oxide and propylene oxide on clean and oxygen precovered Ag(110) was studied using temperature programmed desorption, low-energy electron diffraction (LEED), high-resolution electron energy-loss spectroscopy (HREELS), and x-ray photoelectron spectroscopy. Both ethylene oxide (C2H4O) and propylene oxide (C3H6O) adsorb weakly on the clean Ag(110) surface, with heats of adsorption of 9.5 and 10.6 kcal/mol, respectively. The heats of adsorption of both C2H4O and C3H6O increase by about 30% as the coverage of coadsorbed atomic oxygen is increased up to an oxygen coverage of 0.5, where the heat of adsorption decreases again. Ethylene oxide forms a c(2×2) LEED pattern at saturation coverage of the monolayer following adsorption at 90 K. A racemic mixture of C3H6O forms a (4×2)p1g1 LEED pattern, while the pure enantiomer (S)-C3H6O forms a c(2×2) pattern at the same saturation coverage of the monolayer. Models of the structures accounting for these data are proposed. The HREELS of C2H4O and C3H6O on clean Ag(110) are little perturbed from their gas phase spectra. The epoxide ring of C2H4O is close to normal to the surface, while that of C3H6O is inclined. There is little change in the vibrational frequencies of the normal modes of C2H4O or C3H6O on the oxygen precovered surface. The orientation of C3H6O is influenced by coadsorbed atomic oxygen.
Luminescent and Magnetic Nanoparticulates as Biomarkers (2010)

Non invasive imaging modalities such as computed x-ray tomography, ultrasound, magnetic resonance imaging and positron emission tomography are used clinically for diagnostic medical applications. Contrast agents are frequently used for providing better spatial resolution with higher sensitivities. In recent years, advances in the field of nanotechnology have further fueled the research and development of contrast agents and introduced nanoplatforms to obtain sensitive imagery and detect changes at cellular and molecular level. Nanoparticles such as fluorescent silica, quantum dots, iron oxides, magnetically and optically labeled liposomes, dendrimers are routinely employed in research investigations. A rising trend in this area is the development and use of multimodal contrast agents which enable multiple imaging modalities using a single entity and offer the possibility of improved diagnostics, preclinical research and therapeutic monitoring. This review paper focuses on the synthesis and application of optical and magnetic nanoparticulate probes and their integration into single multimodal nanoparticulate entities.
Understanding the mechanism of warfarin-mediated PC prevention. (2016)

e635 Background: Multi-institution retrospective trials have shown that prolonged use of warfarin reduces the risk of prostate cancer (PC), an effect that is not observed for other cancers. The anti-coagulant warfarin prevents the gamma-carboxylation (gla) of target proteins by interfering with the vitamin K cycle through its inhibition of the vitamin K epoxide reductase (VKOR). Most known gla proteins are found in the clotting cascade, but here we investigate the role of gla of the androgen receptor (AR) and other warfarin-mediated effects in the prevention of PC by warfarin. Methods: We treated mice with warfarin and performed RNA-seq on prostate tissues. We used immunoprecipitation (IP) followed by mass spec sequencing to identify gla sites on AR. We used cell culture models to investigate the role of AR-gla and other pathways identified by RNA-seq data in the mechanism of action of warfarin. Finally, we sequenced a SNP in VKOR and performed IHC to detect VKOR expression in prostatectomy tissues in an institutional series. Results: RNA-seq data show alteration of several pathways in warfarin-treated mouse prostates, including AR signaling, hormone and lipid synthesis, and genes known to affect PC (e.g. SPINK1). Mass spec shows that AR is gla’d at amino acid 2E, which is known to be mutated in partial androgen insensitivity syndrome patients. Warfarin inhibits AR conformation change and transcriptional activity in benign (non-cancerous) prostate cells. VKOR knock-down recapitulates effects of warfarin treatment, suggesting an on target effect of the drug. Mutation of the AR-gla site has modest effects in benign prostate cells. In a small series of patients, we found that one allele of a VKOR SNP is found at a significantly higher rate in PC patients than expected. We also found that VKOR is highly expressed in normal human prostate epithelia but is lost in cancerous tissue, a pattern of expression that is unique to PC. Conclusions: Warfarin, likely through its ability to control AR-gla, inhibits AR transcriptional activity. The relative contribution of modest AR inhibition and the effect on other pathways must be investigated to determine how warfarin reduces the risk of PC and to identify optimal drug targets for development of chemopreventative therapeutics.