gebhart/patrepeval huggingface dataset:
Vaccination with irradiated autologous melanoma cells engineered to secrete human granulocyte–macrophage colony-stimulating factor generates potent antitumor immunity in patients with metastatic melanoma (1998)

We conducted a Phase I clinical trial investigating the biologic activity of vaccination with irradiated autologous melanoma cells engineered to secrete human granulocyte-macrophage colony-stimulating factor in patients with metastatic melanoma. Immunization sites were intensely infiltrated with T lymphocytes, dendritic cells, macrophages, and eosinophils in all 21 evaluable patients. Although metastatic lesions resected before vaccination were minimally infiltrated with cells of the immune system in all patients, metastatic lesions resected after vaccination were densely infiltrated with T lymphocytes and plasma cells and showed extensive tumor destruction (at least 80%), fibrosis, and edema in 11 of 16 patients examined. Antimelanoma cytotoxic T cell and antibody responses were associated with tumor destruction. These results demonstrate that vaccination with irradiated autologous melanoma cells engineered to secrete granulocyte-macrophage colony-stimulating factor stimulates potent antitumor immunity in humans with metastatic melanoma.
Nasopharyngeal Carriage of Antibiotic-Resistant Haemophilus influenzae in Healthy Children (1979)

We selected 16 schools representing a broad socioeconomic cross-section of metropolitan Omaha and obtained nasopharyngeal cultures for Haemophilus influenzae from 1,084 healthy 4- to 7-year-old children. We found that 34.2% of the children carried nontypable strains and 2.0% carried type b strains. Carriage rates were not influenced by recent illness, family size, or number of people sharing a bedroom. The prevalence of ampicillin-resistant H influenzae in the sample population was 0.9% for nontypable strains and 0.4% for type b strains; it was not significantly different in the group of children who had recently used beta-lactam antibiotics. One child carried a nontypable strain which was resistant to both chloramphenicol and tetracycline, the first chloramphenicol-resistant H influenzae detected in Omaha. A survey of healthy children may be a useful method for projecting a community's risk of disease caused by ampicillin-resistant H influenzae. Among the nasopharyngeal isolates from healthy children, 2.7% of nontypable strains and 18.2% of type b strains were resistant to ampicillin (P less than .01). During the same five-month period in Omaha, clinical failure in the treatment of otitis media with ampicillin was uncommon and four (20.0%) of 20 cases of H influenzae type b bacteremia and meningitis were caused by ampicillin-resistant organisms.
On the Stability of Double Stranded Nucleic Acids (2001)

We present the first pressure-versus-temperature phase diagram for the helix-to-coil transition of double stranded nucleic acids. The thermodynamic stability of a nucleic acid duplex is a complex function of temperature and pressure and strongly depends on the denaturation temperature, T(M), of the duplex at atmospheric pressure. Depending upon T(M), pressure, and temperature, the phase diagram shows that pressure may stabilize, destabilize, or have no effect on the conformational state of DNA. To verify the phase diagram, we have conducted high-pressure UV melting experiments on poly(dIdC)poly(dIdC), a DNA duplex, poly(rA)poly(rU), an RNA duplex, and poly(dA)poly(rU), a DNA/RNA hybrid duplex. The T(M) values of these duplexes have been modulated by altering the solution ionic strength. Significantly, at low salt, these three duplexes have helix-to-coil transition temperatures of 50 degrees C or less. In agreement with the derived phase diagram, we found that the polymeric duplexes were destabilized by pressure if the T(M) is < approximately 50 degrees C. However, these duplexes were stabilized by pressure if the T(M) is > approximately 50 degrees C. The DNA/RNA hybrid duplex, poly(dA)poly(rU), with a T(M) of 31 degrees C in 20 mM NaCl undergoes a pressure-induced helix-to-coil transition at room temperature. This is the first report of pressure-induced denaturation of a nucleic acid duplex and provides new insights into the molecular forces stabilizing these structures.
Controlling Messenger RNA Stability in Bacteria: Strategies for Engineering Gene Expression (1997)

Recent advances in the understanding of prokaryotic gene expression have led scientists to look beyond traditional promoter control for new methods of regulating gene expression. A promising, new technique centers on controlling the stability of messenger RNA. To exploit the potential of mRNA stability for gene expression control, it is important to understand the mechanisms of prokaryotic mRNA decay as well as the cellular factors that can be used to enhance bacterial gene expression through mRNA stabilization. Factors involved in controlling prokaryotic mRNA stability such as nucleases, secondary structures, translation influences, and transcription effects are discussed and analyzed within the context of three prevailing mRNA decay theories. Several strategies for manipulating mRNA stability in genetically-engineered cells are developed from these discussions and presented as a future direction in gene expression control. In the near future, it should be possible to use these strategies to control mRNA stability in such applications as pharmaceutical protein production and metabolic pathway design.
A Naturally Occurring Mutation of the Opsin Gene (T4R) in Dogs Affects Glycosylation and Stability of the G Protein-coupled Receptor (2004)

Rho (rhodopsin; opsin plus 11-cis-retinal) is a prototypical G protein-coupled receptor responsible for the capture of a photon in retinal photoreceptor cells. A large number of mutations in the opsin gene associated with autosomal dominant retinitis pigmentosa have been identified. The naturally occurring T4R opsin mutation in the English mastiff dog leads to a progressive retinal degeneration that closely resembles human retinitis pigmentosa caused by the T4K mutation in the opsin gene. Using genetic approaches and biochemical assays, we explored the properties of the T4R mutant protein. Employing immunoaffinity-purified Rho from affected RHO(T4R/T4R) dog retina, we found that the mutation abolished glycosylation at Asn(2), whereas glycosylation at Asn(15) was unaffected, and the mutant opsin localized normally to the rod outer segments. Moreover, we found that T4R Rho(*) lost its chromophore faster as measured by the decay of meta-rhodopsin II and that it was less resistant to heat denaturation. Detergent-solubilized T4R opsin regenerated poorly and interacted abnormally with the G protein transducin (G(t)). Structurally, the mutation affected mainly the "plug" at the intradiscal (extracellular) side of Rho, which is possibly responsible for protecting the chromophore from the access of bulk water. The T4R mutation may represent a novel molecular mechanism of degeneration where the unliganded form of the mutant opsin exerts a detrimental effect by losing its structural integrity.
Regulation of murine B cells through surface immunoglobulin. I. Monoclonal anti-delta antibody that induces allotype-specific proliferation. (1980)

We describe the identification of a monoclonal antibody that recognizes a determinant on the delta chain of mice of the Iga, allotype groups. The monoclonal Ig in soluble form induces allotype-specific proliferation by splenic B lymphocytes from normal animals of these haplotypes. Spleen cells from mice bearing the X-linked defect of CBA/N mice fail to respond, although they bear the determinant. Proliferation is independent of T lymphocytes. The data indicate a direct triggering function for sIgD.
Highly efficient (GaAl)As buried-heterostructure lasers with buried optical guide (1979)

A new buried-heterostructure laser with a buried optical guide has been developed. A threshold current around 20 mA and a differential quantum efficiency as high as 85% are obtained under cw operation. This results in highly efficient laser operation, i.e., 35% power conversion efficiency at an optical output of 15 mW per facet, at which no degradation is observed over 3000 h at room temperature. Stable lowest-order transverse mode and nearly isotropic laser beam (∼25°×35°) are obtained. Second-order harmonic distortion is 55–65 dB below the fundamental level for 30% modulation with a 100-MHz sinusoidal signal at 5 mW.
Investigation of optimum pilot channel structure for VSF-OFCDM broadband wireless access in forward link (2004)

This paper clarifies the optimum pilot channel structure in the broadband forward link for variable spreading factor-orthogonal frequency and code division multiplexing (VSF-OFCDM) wireless access using two-dimensional spreading while taking into account the following factors that affect radio link performance: (1) channel estimation accuracy for coherent detection, (2) the accuracy of the signal-to-interference power ratio (SIR) measurement for adaptive modulation and channel coding and the reliability information of the received signals, (3) the configuration of simultaneously multiplexed orthogonal pilot patterns, and (4) the impact on cell search, as well as flexibility in allocating transmission power resources. We show that although the time-multiplexed and code-multiplexed structure achieves almost the same channel estimation accuracy, the code-multiplexed structure is more advantageous due to flexible multiplexing of the orthogonal pilot patterns within one sub-carrier resulting from the accommodation of numerous OFCDM symbols in a frame. Assuming the use of an adaptive antenna array beam-forming transmitter where many orthogonal pilot patterns are required, we clarify that the cod-multiplexed structure achieves more accurate SIR measurement compared to the time-multiplexed structure. Meanwhile, the time-multiplexed structure is advantageous in that it does not require an exclusive synchronization channel for cell search. Consequently, we elucidate that the code-multiplexed structure is overall slightly superior to the time-multiplexed structure because the code-multiplexed pilot channel structure is advantageous in that it can flexibly share transmission power resources among other physical channels, thereby resulting in increasing the number of orthogonal pilot patterns and increasing the number of simultaneous packet channels despite obtaining almost the identical merits of the time-multiplexed structure from the viewpoint of radio link performance.
Mannose-Binding Lectin and Mortality in Type 2 Diabetes (2006)

In patients with type 2 diabetes, measurements of MBL alone or in combination with CRP can provide prognostic information on mortality and the development of albuminuria.
Development and Characterization of Biphenylsulfonamides as Novel Inhibitors of Bone Resorption (2006)

Increased osteoclastic bone resorption plays a central role in the pathogenesis of many bone diseases, and osteoclast inhibitors are the most widely used treatments for these diseases. We have identified and characterized a series of novel biphenylsulfonamide derivatives that have potent inhibitory effects on osteoclastic bone resorption in vitro and that prevent ovariectomy-induced bone loss in vivo. A number of aromatic substituted derivatives were prepared and a QSAR model was generated, which allowed accurate prediction of compound potency. Using this model, we have prepared compounds able to inhibit osteoclast formation and bone resorption in vitro at concentrations in the nanomolar range. One such compound, 55 (ABD295) (Greig, I. R.; Mohamed, A. I.; Ralston, S. H.; van't Hof, R. J. Alkyl Aryl Sulfonamides as Therapeutic Agents for the Treatment of Bone Conditions. GB Patent WO2005118528, 2005), fully reversed ovariectomy-induced bone loss in mice at a dose of 5 (mg/kg)/day. In conclusion, biphenylsulfonamides like 55 form a new class of potent antiresorptive agents with possible therapeutic use in diseases characterized by increased bone resorption.
WiFi-SLAM Using G aussian Process Latent Variable Models (2007)

WiFi localization, the task of determining the physical location of a mobile device from wireless signal strengths, has been shown to be an accurate method of indoor and outdoor localization and a powerful building block for location-aware applications. However, most localization techniques require a training set of signal strength readings labeled against a ground truth location map, which is prohibitive to collect and maintain as maps grow large. In this paper we propose a novel technique for solving the WiFi SLAM problem using the Gaussian Process Latent Variable Model (GP-LVM) to determine the latent-space locations of unlabeled signal strength data. We show how GP-LVM, in combination with an appropriate motion dynamics model, can be used to reconstruct a topological connectivity graph from a signal strength sequence which, in combination with the learned Gaussian Process signal strength model, can be used to perform efficient localization. 1
Prosthetic Disc Replacement: The Future? (2002)

Since it first was introduced more than 90 years ago, disc arthrodesis remains the main surgical method for the treatment of degenerative disc disease. Although this procedure does relatively well in stabilizing the anterior column and relieving low back pain by eliminating motion, it is not physiologic and it alters the stress distribution on the adjacent segments. Although the issue of whether this stress alteration leads to symptomatic degeneration remains debatable, it probably is agreed that disc arthrodesis is not the best choice for correcting or preventing anterior column instability caused by degenerative disc disease. The ultimate solution for reestablishing anterior column stability is to restore not only the anatomy but also the normal mechanical function by using a more functional device, prosthetic disc replacement. During the past 401 years, many different designs have been attempted for prosthetic disc replacement. Many biomechanical studies have shown that normal mechanical functions of a disc can be restored by a disc prosthesis. Some early clinical studies have shown promising results. Although it might take more effort to optimize the design and reduce costs and risks, prosthetic disc replacement will be the future of spine care.
Regulation of katF and katE in Escherichia coli K-12 by weak acids (1992)

Chromosomal transcriptional and translational lacZ fusions to the katE (structural gene for the HPII hydroperoxidase) and katF (putative sigma factor required for katE expression) genes of Escherichia coli were isolated, and the regulation of these fusions was used to identify factors that control the expression of these two important antioxidant factors. While katE was found to be regulated primarily at the level of transcription (since induction patterns were similar for both transcriptional and translational fusions), katF expression was a function of both transcriptional and translational signals. The katE gene was induced 57-fold as cells entered the stationary phase, while katF was induced 23-fold. katF induction was coincident with katE induction and occurred at the onset of the stationary growth phase. Expression of both katE and katF could be induced by resuspending uninduced exponential-phase cells in spent culture supernatant recovered from stationary-phase cells. The component of stationary-phase culture supernatant responsible for induction of the katF regulon appeared to be acetate, since expression of both katE and katF fusions was induced when exponential-phase cells were exposed to this weak acid. Other weak acids, including propionate and benzoate, were also found to be effective inducers of expression of both katF and katE. Induction of katE and katF fusions was unaffected in merodiploid strains containing both mutant and wild-type alleles, indicating that expression of both genes is independent of the wild-type gene product. Examination of catalase zymograms prepared from cells exposed to various levels of acetate revealed that both HPI and HPII catalases are induced by this weak acid, suggesting that there is a common link in the regulation of these two enzymes.
GPU-Enabled Particle Based Optimization for Robotic-Hand Pose Estimation and Self-Calibration (2015)

Humanoid robots have complex kinematic chains that are difficult to model with the precision required to reach and/or grasp objects properly. In this paper we propose a GPU-enabled vision based 3D hand pose estimation method that runs during robotic reaching tasks to calibrate in real time the kinematic chain of the robot arm. This is achieved by combining: i) proprioceptive and visual sensing, and ii) a kinematic and computer graphics model of the system. We use proprioceptive input to create visual hypotheses about the hand appearance in the image using a 3D CAD model inside the game engine from Unity Technologies. These hypotheses are compared with the actual visual input using particle filter techniques. The outcome of this processing is the best hypothesis for the hand pose and a set of joint offsets to calibrate the arm. We tested our approach in a simulation environment and verified that the angular error is reduced 3 times and the position error about 12 times comparing with the non-calibrated case (proprioception only). The used GPU implementation techniques ensures a performance 2.5 times faster than performing the computations on the CPU.
Molecular recognition by mass spectrometry (2005)

A recent major advance in the field of mass spectrometry in the biomolecular sciences is represented by the study of the supramolecular interactions among two or more partners in the gas phase. A great deal of chemistry and most of biochemistry concerns molecular interactions taking place in solution. The electrospray technique, which allows direct sampling from solution, and soft ionization of the solute without deposition into the analyte of large amounts of energy, guarantees in many cases the survival of noncovalent bondings and, hence, the direct analysis of the supramolecular complexes present in the condensed phase. The proper preparation of the solution to be studied and also the expert and accurate setting and use of the instrumental parameters are the prerequisites for gaining results as to the specific interactions between, for instance, a protein conformationally modified by its specific metal ion, eventually, and a ligand molecule. The analysis of the charge state of the protein itself and of the modifications of the complex integrity by activating collisions are also methods for studying the biomolecule-molecule interactions. Accordingly, this new mass spectrometric approach to the supramolecular chemistry, which could be also defined as 'supramolecular mass spectrometry', allows the study of ion-protein, protein-protein, protein-ligand and DNA-drug interactions. Chiral recognition can also be performed in the gas phase, studying by electrospray mass spectrometry the fragmentation of diastereomeric complex ions. Not the least, a deep insight can also be obtained into the formation and nature of inclusion complexes like those formed with crown ethers, cyclodextrins and calixarenes as host molecules. All these topics are treated to a certain extent in this special feature article.
Progressive retinal atrophy: a model for retinitis pigmentosa in companion animals. (1994)

Plasma lactate measurements are typically performed in real time, limiting their usefulness in multicenter or longitudinal studies. To determine the stability of lactate specimens, blood was drawn in sodium fluoride/potassium oxalate tubes from 13 volunteers before and after 5 min of handgrip exercise to intentionally increase lactate concentrations. Plasma was stored at -70 degrees C. Aliquots were assayed in real time and after 1, 3, 6, 9, 12, 18, and 24 months. Real-time lactate concentrations measured at baseline ranged from 0.52 to 2.23 mmol/L before and from 2.91 to 11.04 mmol/L after handgrip exercise. Using a linear mixed model, the estimated change from baseline at month 24 was 1.67% (95% confidence interval, -0.70% to 4.03%) for pre-exercise samples and 0.39% (95% CI, -1.13% to 1.91%) for post-exercise samples. Stored serial specimens from 232 HIV-infected subjects in a multicenter trial of antiretroviral therapy were also assayed centrally. Among those, median plasma lactate increased from baseline to 64 weeks by 0.4 mmol/L with zidovudine+lamivudine treatment and by 0.6 mmol/L with didanosine+stavudine (each p<0.001 from baseline; p=0.04 for difference between groups over time). When performed as in this study, frozen storage with central batch lactate analysis is appropriate for prospectively collected samples in multicenter trials.
In-Vehicle CAN Message Authentication: An Evaluation Based on Industrial Criteria (2017)

Vehicles have evolved from mostly mechanical machines into devices controlled by an internal computer network consisting of more than 100 interconnected Electronic Control Units (ECUs). Moreover, modern vehicles communicate with external devices to enable new features, but these new communication facilities also expose safety-critical functions to security threats. As the most prevalent automotive bus, the Controller Area Network (CAN) bus is a prime target for attacks. Even though the computer security community has proposed several message authentication solutions to alleviate those threats, such solutions have not yet been widely adopted by the automotive industry. We have identified the most promising CAN message authentication solutions and provide a comprehensive overview of them. In order to investigate the lack of adoption of such solutions, we, together with industry experts, have identified five general requirements they must fulfill in order to be considered viable in industry. Based on those requirements, we analyze and evaluate the identified authentication solutions. We find that none of them meet all the requirements, and that backward compatibility and acceptable overhead are the biggest obstacles.
A common molecular basis for rearrangement disorders on chromosome 22q11 (1999)

The chromosome 22q11 region is susceptible to rearrangements that are associated with congenital anomaly disorders and malignant tumors. Three congenital anomaly disorders, cat-eye syndrome, der() syndrome and velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS) are associated with tetrasomy, trisomy or monosomy, respectively, for part of chromosome 22q11. VCFS/DGS is the most common syndrome associated with 22q11 rearrangements. In order to determine whether there are particular regions on 22q11 that are prone to rearrangements, the deletion end-points in a large number of VCFS/DGS patients were defined by haplotype analysis. Most VCFS/DGS patients have a similar 3 Mb deletion, some have a nested distal deletion breakpoint resulting in a 1.5 Mb deletion and a few rare patients have unique deletions or translocations. The high prevalence of the disorder in the population and the fact that most cases occur sporadically suggest that sequences at or near the breakpoints confer susceptibility to chromosome rearrangements. To investigate this hypothesis, we developed hamster-human somatic hybrid cell lines from VCFS/DGS patients with all three classes of deletions and we now show that the breakpoints occur within similar low copy repeats, termed LCR22s. To support this idea further, we identified a family that carries an interstitial duplication of the same 3 Mb region that is deleted in VCFS/DGS patients. We present models to explain how the LCR22s can mediate different homologous recombination events, thereby generating a number of rearrangements that are associated with congenital anomaly disorders. We identified five additional copies of the LCR22 on 22q11 that may mediate other rearrangements leading to disease.