gebhart/patrepeval huggingface dataset:
Rotational Changes at the Knee after ACL Injury Cause Cartilage Thinning (2006)

We examined the relationship between specific gait changes after anterior cruciate ligament injury and the progression of osteoarthritis at the knee. The study was done using a finite-element model derived from subject specific three-dimensional cartilage volumes created from magnetic resonance images. Cartilage thinning was predicted using an iterative algorithm based on the octahedral shear stress. Simulations were done for a knee with normal alignment and for a knee with an internal tibial rotation offset, as associated with anterior cruciate ligament deficiency. For the healthy knee, the model predicted patterns of cartilage thinning consistent with a previous clinical report of idiopathic osteoarthritis. For the ACL-deficient scenario the model predicted a more rapid rate of cartilage thinning throughout the knee, especially in the medial compartment. The results suggest that the progression of osteoarthritis after anterior cruciate ligament injury is associated with a shift in the normal load bearing regions of the knee joint during normal function due to kinematic changes, and highlight the importance of restoring proper gait during anterior cruciate ligament reconstruction.
Cyclin synthesis: Who needs it? (1993)

Studies of the G2 to M transition in amphibian oocytes, in combination with in vitro mitotic systems and yeast genetic analysis, have significantly contributed to our understanding of the mechanisms by which M-phase is regulated. Historically, oocyte maturation has provided a number of valuable initial observations, but the biochemical elucidation of cell cycle control mechanisms has proved more tractable in cell-free extracts of frog eggs which reproduce aspects of early embryogenic mitosis. Recent experiments examining the importance of protein synthesis in the maturing oocyte have highlighted some important differences between mitosis and meiosis. Additional controls found in meiosis but not embryonic mitosis, are similar to controls found in somatic cells. This suggests that understanding the differences, as well as the similarities, between meiosis in the oocyte and mitosis in the early embryo will help us to learn more about the way in which cells enter and leave mitosis.
Joint Sparse Concentric Array Design for Frequency and Rotationally Invariant Beampattern (2020)

Frequency-invariant concentric arrays are fundamental components in some real-world applications, like teleconferencing, voice service devices, underwater acoustics, and others, where the azimuthal arrival direction of the desired signal is varying. The fact that the demand for limited hardware and computational resources in such applications is essential, motivates the use of a sparse design which can optimize both the number of the required sensors and the complex weights of the beamformer. Herein, we propose a new greedy based joint-sparse design of frequency and rotationally invariant concentric arrays which preserves the properties of the designed directivity pattern for different azimuthal directions of steering. Simulation results show that the greedy sparse design, compared to uniform and random designs, gives superior performance in terms of array gain, and frequency and rotationally invariant beampattern, with a reasonable computational and hardware resources.
Major histocompatibility complex class II‐restricted presentation of a cytosolic antigen by autophagy (2003)

Biochemical and functional studies have demonstrated major histocompatibility complex (MHC) class II-restricted presentation of peptides derived from cytosolic proteins, but the underlying processing and presentation pathways have remained elusive. Here we show that endogenous presentation of an epitope derived from the cytosolic protein neomycin phosphotransferase II (NeoR) on MHC class II is mediated by autophagy. This presentation pathway involves the sequestration of NeoR into autophagosomes, and subsequent delivery into the lytic compartment. These results identify endosomes/lysosomes as the processing compartment for cytosolic antigens and furthermore link endogenous antigen presentation on MHC class II with the process of cellular protein turnover by autophagy.
High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias (2010)

In order to develop a xenograft model to determine the efficacy of new therapies against primary human precursor-B acute lymphoblastic leukemia (ALL) stem cells (LSCs), we used the highly immunodeficient non-obese diabetic (NOD).Cg-Prkdc(scid)IL2rg(tmlWjl)/SzJ (NOD-severe combined immune deficient (scid) IL2rg(-/-)) mouse strain. Intravenous transplantation of 2 of 2 ALL cell lines and 9 of 14 primary ALL cases generated leukemia-like proliferations in recipient mice by 1-7 months after transplant. Leukemias were retransplantable, and the immunophenotypes, gene rearrangements and expression profiles were identical or similar to those of the original primary samples. NOD-scid mice transplanted with the same primary samples developed similar leukemias with only a slightly longer latency than did NOD-scid-IL2Rg(-/-) mice. In this highly sensitive NOD-scid-IL2Rg(-/-)-based assay, 1-100 unsorted primary human ALL cells from five of five tested patients, four of whom eventually experienced leukemia relapse, generated leukemias in recipient mice. This very high frequency of LSCs suggests that a hierarchical LSC model is not valuable for poor-outcome ALL.
Chemical Synthesis and NMR Solution Structure of Conotoxin GXIA from Conus geographus (2021)

Conotoxins are disulfide-rich peptides found in the venom of cone snails. Due to their exquisite potency and high selectivity for a wide range of voltage and ligand gated ion channels they are attractive drug leads in neuropharmacology. Recently, cone snails were found to have the capability to rapidly switch between venom types with different proteome profiles in response to predatory or defensive stimuli. A novel conotoxin, GXIA (original name G117), belonging to the I<sub>3</sub>-subfamily was identified as the major component of the predatory venom of piscivorous <i>Conus geographus</i>. Using 2D solution NMR spectroscopy techniques, we resolved the 3D structure for GXIA, the first structure reported for the I<sub>3</sub>-subfamily and framework XI family. The 32 amino acid peptide is comprised of eight cysteine residues with the resultant disulfide connectivity forming an ICK+1 motif. With a triple stranded β-sheet, the GXIA backbone shows striking similarity to several tarantula toxins targeting the voltage sensor of voltage gated potassium and sodium channels. Supported by an amphipathic surface, the structural evidence suggests that GXIA is able to embed in the membrane and bind to the voltage sensor domain of a putative ion channel target.
Dual Role of the Leukocyte Integrin αMβ2 in Angiogenesis (2014)

Polymorphonuclear neutrophils (PMNs) and macrophages are crucial contributors to neovascularization, serving as a source of chemokines, growth factors, and proteases. α(M)β(2)(CD11b/CD18) and α(L)β(2)(CD11a/CD18) are expressed prominently and have been implicated in various responses of these cell types. Thus, we investigated the role of these β2 integrins in angiogenesis. Angiogenesis was analyzed in wild-type (WT), α(M)-knockout (α(M)(-/-)), and α(L)-deficient (α(L)(-/-)) mice using B16F10 melanoma, RM1 prostate cancer, and Matrigel implants. In all models, vascular area was decreased by 50-70% in α(M)(-/-) mice, resulting in stunted tumor growth as compared with WT mice. In contrast, α(L) deficiency did not impair angiogenesis and tumor growth. The neovessels in α(M)(-/-) mice were leaky and immature because they lacked smooth muscle cell and pericytes. Defective angiogenesis in the α(M)(-/-) mice was associated with attenuated PMN and macrophage recruitment into tumors. In contrast to WT or the α(L)(-/-) leukocytes, the α(M)(-/-) myeloid cells showed impaired plasmin (Plm)-dependent extracellular matrix invasion, resulting from 50-75% decrease in plasminogen (Plg) binding and pericellular Plm activity. Surface plasmon resonance verified direct interaction of the α(M)I-domain, the major ligand binding site in the β(2) integrins, with Plg. However, the α(L)I-domain failed to bind Plg. In addition, endothelial cells failed to form tubes in the presence of conditioned medium collected from TNF-α-stimulated PMNs derived from the α(M)(-/-) mice because of severely impaired degranulation and secretion of VEGF. Thus, α(M)β(2) plays a dual role in angiogenesis, supporting not only Plm-dependent recruitment of myeloid cells to angiogenic niches, but also secretion of VEGF by these cells.
Imaging activated T cells predicts response to cancer vaccines (2018)

In situ cancer vaccines are under active clinical investigation, given their reported ability to eradicate both local and disseminated malignancies. Intratumoral vaccine administration is thought to activate a T cell-mediated immune response, which begins in the treated tumor and cascades systemically. In this study, we describe a PET tracer (64Cu-DOTA-AbOX40) that enabled noninvasive and longitudinal imaging of OX40, a cell-surface marker of T cell activation. We report the spatiotemporal dynamics of T cell activation following in situ vaccination with CpG oligodeoxynucleotide in a dual tumor-bearing mouse model. We demonstrate that OX40 imaging was able to predict tumor responses on day 9 after treatment on the basis of tumor tracer uptake on day 2, with greater accuracy than both anatomical and blood-based measurements. These studies provide key insights into global T cell activation following local CpG treatment and indicate that 64Cu-DOTA-AbOX40 is a promising candidate for monitoring clinical cancer immunotherapy strategies.
Modelling an Energy-Dispersive X-Ray Diffraction System for Drug Detection (2009)

A system for drug detection using X-ray diffraction is currently being developed by the DILAX collaboration. A simulation program for modelling the response of an energy-dispersive X-ray diffraction system has been developed, with the two-fold aim of selecting possible configurations prior to experimental tests and of generating data for statistical models for prediction of drug content. Simulated data showed a good agreement with experimental results. The data showed that the main factor affecting the shape of the diffraction pattern is the thickness of the sample. Scatter angle and detector energy resolution have a smaller effect on the diffraction pattern. This suggests that cheaper, room-temperature detectors can be used for a drug detection system without any loss in sensitivity and specificity.
Development of a 250kW PV PCS and adaptive MPPT method (2010)

This paper presents the hardware configuration of a developed 250kW photovoltaic (PV) power conditioning system (PCS) and shows the efficiency curve both with transformer and without transformer. Also, adaptive maximum power point tracking (MPPT) method is proposed and it tracks the accurate maximum power point (MPP) during the fast changing environmental conditions. The proposed method is verified through simulations and a scaled-down experiment.
Regadenoson for the treatment of COVID-19: A five case clinical series and mouse studies (2023)

Infused RA is safe and produces rapid anti-inflammatory effects mediated by A2A adenosine receptors on iNKT cells and possibly in part by A2ARs on other immune cells and platelets. We speculate that iNKT cells are activated by release of injury-induced glycolipid antigens and/or alarmins such as IL-33 derived from virally infected type II epithelial cells which in turn activate iNKT cells and secondarily other immune cells. Adenosine released from hypoxic tissues, or RA infused as an anti-inflammatory agent decrease proinflammatory cytokines and may be useful for treating cytokine storm in patients with Covid-19 or other inflammatory lung diseases or trauma.
Surface Analysis of Electrodes from Cells Containing Electrolytes with Stabilizing Additives Exposed to High Temperature (2008)

We have conducted a detailed investigation of the effect of thermal stabilizing additives, including dimethyl acetamide (DMAc), N-methyl pyrrolidone, vinylene carbonate (VC), and vinylethylene carbonate (VEC), on the reactions of the electrolyte with the surface of the electrodes in lithium-ion cells. Cells were constructed with mesocarbon microbead anodes, LiNi 0.8Co0.2O2 cathodes, and 1.0 M LiPF6 in 1:1:1 ethylene carbonate/diethyl carbonate/dimethyl carbonate electrolyte with and without electrolyte additives. The cells were stored sequentially at 55, 60, and 65°C for 10 days at each temperature. The cells were then dismantled, and the surfaces of the electrodes were analyzed via a combination of infrared spectroscopy with attenuated total reflection, X-ray photoelectron spectroscopy, and scanning electron microscope-energy dispersive spectroscopy. The surface of the electrodes extracted from cells containing the baseline electrolyte contained thick surface films composed of electrolyte decomposition products. The addition of 1% DMAc inhibits the reaction of the electrolyte with surface of the electrodes, especially on the anode. The addition of 1.5% VC results in the formation of poly(vinylene carbonate) on both electrodes and inhibits the reaction of electrolyte with the electrodes, especially the cathode. The addition of 1.5% VEC or 10% DMAc did not significantly impede the reaction of the electrolyte with the electrodes. © 2008 The Electrochemical Society.
Natural chaperonin of the hyperthermophilic archaeum, Thermococcus strain KS‐1: a hetero‐oligomeric chaperonin with variable subunit composition (2001)

To study the difference in expression of the chaperonin alpha- and beta-subunits in Thermococcus strain KS-1 (T. KS-1), we measured their intracellular contents at various growth temperatures using subunit-specific antibodies. The beta-subunit was significantly more abundant with increasing temperature (maximum at 93 degrees C), whereas the alpha-subunit was not. Native PAGE with Western blot analysis indicated that the natural chaperonins in the crude extracts of T. KS-1 cells grown between 65 degrees C and 95 degrees C migrate as single bands with different mobility. The recombinant alpha- and beta-subunit homo-oligomers migrated differently from each other and from natural chaperonins. Immunoprecipitation also showed that the natural chaperonin was the hetero-oligomer. These results indicate that chaperonin in T. KS-1 formed a hetero-oligomer with variable subunit composition, and that the beta-subunit may be adapted to a higher temperature than the alpha-subunit. T. KS-1 probably changes its chaperonin subunit composition to acclimatize to the ambient temperature.
Treatment of older patients with acute myeloid leukemia (AML): a Canadian consensus. (2013)

Patients over age 60 comprise the majority of those diagnosed with acute myeloid leukemia (AML), but treatment approaches in this population are variable, with many uncertainties and controversies. Our group conducted a literature review to summarize the latest information and to develop a consensus document with practical treatment recommendations. We addressed five key questions: selection criteria for patients to receive intensive induction chemotherapy; optimal induction and post-remission regimens; allogeneic hematopoietic stem cell transplantation (HSCT); treatment of patients not suitable for induction chemotherapy; and treatment of patients with prior hematological disorders or therapy-related AML. Relevant literature was identified through a PubMed search of publications from 1991 to 2012. Key findings included the recognition that cytogenetics and molecular markers are major biologic determinants of treatment outcomes in the older population, both during induction therapy and following HSCT. Although disease-specific and patient-specific risk factors for poor outcomes are more common in the older population, age is not in itself sufficient grounds for withholding established treatments, including induction and consolidation chemotherapy. The role of HSCT and use of hypomethylating agents are discussed. Finally, suggested treatment algorithms are outlined, based on these recommendations.
Preclinical toxicology study of liposome encapsulated doxorubicin (TLC D-99): comparison with doxorubicin and empty liposomes in mice and dogs. (1993)

A preclinical toxicology study of intravenously administered liposome encapsulated doxorubicin (TLC D-99), free doxorubicin and empty liposomes was carried out in mice and dogs by single and multiple (daily for 5 days) dose schedules. Single dose intravenous injection studies in mice showed the encapsulated form of doxorubicin to be less toxic (LD50 of 32 mg/kg) than free doxorubicin (LD50 of 17 mg/kg). Toxicity in dogs was evaluated by serial serum chemistry, hematology and EKG analysis, urinalysis, clinical observations, necropsy and histopathologic examination. Empty liposomes injected intravenously into dogs were without significant toxicity. The maximally tolerated dose of free doxorubicin in beagles was 1.5 mg/kg; deaths were seen after a 50% escalation to 2.25 mg/kg. The maximally tolerated dose of liposome encapsulated doxorubicin was higher (2.25 mg/kg); deaths were seen after a 50% escalation to 3.37 mg/kg. A toxicity unique to the encapsulated agent was pyexia (as high as 105.6 degrees F) within twenty four hr of single dosage. This was seen in approximately half of the test animals, was not dose-related, and was not observed in animals that received empty liposomes. The organ specific toxicities seen with TLC D-99 were qualitatively similar to those of free doxorubicin, but less severe.
Hematopoietic Cell Transplantation for Benign Hematological Disorders and Solid Tumors (2003)

Allogeneic hematopoietic cell transplantation (HCT) has been successfully used as replacement therapy for patients with aplastic anemia and hemoglobinopathies. Both autologous and allogeneic HCT following high-dose chemotherapy can correct manifestations of autoimmune diseases. The impressive allogeneic graft-versus-tumor effects seen in patients given HCT for hematological malignancies have stimulated trials of allogeneic immunotherapy in patients with otherwise refractory metastatic solid tumors. This session will update the status of HCT in the treatment of benign hematological diseases and solid tumors. In Section I, Dr. Rainer Storb reviews the development of nonmyeloablative conditioning for patients with severe aplastic anemia who have HLA-matched family members. He also describes the results in patients with aplastic anemia given HCT from unrelated donors after failure of responding to immunosuppressive therapy. The importance of leuko-poor and in vitro irradiated blood product transfusions for avoiding graft rejection will be discussed. In Section II, Dr. Guido Lucarelli reviews the status of marrow transplantation for thalassemia major and updates results obtained in children with class I and class II severity of thalassemia. He also describes results of new protocols for class III patients and efforts to extend HCT to thalassemic patients without HLA-matched family members. In Section III, Dr. Peter McSweeney reviews the current status of HCT for severe autoimmune diseases. He summarizes the results of autologous HCT for systemic sclerosis, multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus, and reviews the status of planned Phase III studies for autologous HCT for these diseases in North America and Europe. He also discusses a possible role of allogeneic HCT in the treatment of these diseases. In Section IV, Dr. Richard Childs discusses the development and application of nonmyeloablative HCT as allogeneic immunotherapy for treatment-refractory solid tumors. He reviews the results of pilot clinical trials demonstrating graft-versus-solid tumor effects in a variety of metastatic cancers and describes efforts to characterize the immune cell populations mediating these effects, as well as newer methods to target the donor immune system to the tumor.
Intervening sequences in human fetal globin genes adopt left-handed Z helices. (1984)

The large intervening sequences ( IVS2 ) of three human fetal globin genes contain tracts of alternating purine-pyrimidine sequences approximately 40-60 base pairs in length which adopt left-handed Z DNA helices under the influence of negative supercoiling. The amount of negative supercoiling (approximately 0.045) required for the right- to left-handed transitions is within the physiological range. The structural aberrations between the right- and left-handed helices were mapped by sequencing the S1 nuclease cleavage sites. Two-dimensional gel electrophoretic analyses of the supercoil-induced relaxation served to characterize the type and length of left-handed structure. Furthermore, binding studies with several types of antibodies confirmed the presence of left-handed helices. Since these simple sequences appear to be hotspots for recombination and gene conversion, unusual DNA conformations may participate in genetic expression.
Biological growth: Reaction, transport and mechanics (2007)

Abstract In this paper, we address some modelling issues related to biological growth. Our treatment is based on a recently-proposed, general formulation for growth (Journal of the Mechanics and Physics of Solids, 52, 2004, 1595– 1625) within the context of open system continuum thermodynamics. We aim to enhance this treatment by making it more appropriate for the biophysics of growth in soft tissue, specifically tendon. This involves several modifications to the mathematical formulation to represent the reactions, transport and mechanics, and their interactions. We also reformulate the governing differential equations for reactiontransport to represent the incompressibility constraint on the fluid phase of the tissue. This revision enables a straightforward implementation of numerical stabilisation for the hyperbolic, or advection-dominated, limit. A finite element implementation employing a staggered scheme is utilised to solve the coupled nonlinear partial differential equations that arise from the theory. Motivated by our experimental model, an in vitro scaffold-free engineered tendon formed by selfassembly of tendon fibroblasts (Calve et al., 2004), we solve several numerical examples demonstrating biophysical aspects of growth, and the improved numerical performance of the models.
An International Perspective on Abnormal Uterine Bleeding (2011)

This series of eight articles on various aspects of abnormal uterine bleeding (AUB) is the result of several thousand man- and woman-hours of review of multiple clinical, scientific, and social issues around the broad topic of AUB. The process was initiated because of an increasing awareness of the poor and confused definitions of several of the traditional English-language terminologies, especially menorrhagia, metrorrhagia, and dysfunctional uterine bleeding. Over the past 6 to 7 years, many stakeholders have participated in three major workshops, numerous conferences, teleconferences, and other meetings leading to a series of publications, identification of key issues, and presentation of recommendations on terminologies, definitions, and classifications around AUB. The articles in this issue of Seminars distill into written word this exercise, and we are grateful to many colleagues for their valuable input.
High Bandwidth Large Core Multimode Fibre with High Connector Tolerance for Short Distance Communications (2020)

We propose a large core multimode fibre for short distance communications. We demonstrated 24 GHz·km peak modal bandwidth in the 850 nm window, connector offset tolerance up to 10 μm, and 25G error-free multimode VCSEL transmission over 500 m of such fibre.