gebhart/patrepeval huggingface dataset:
Rhodopsin Mutants That Bind But Fail to Activate Transducin (1990)

Rhodopsin is a member of a family of receptors that contain seven transmembrane helices and are coupled to G proteins. The nature of the interactions between rhodopsin mutants and the G protein, transduction (Gt), was investigated by flash photolysis in order to monitor directly Gt binding and dissociation. Three mutant opsins with alterations in their cytoplasmic loops bound 11-cis-retinal to yield pigments with native rhodopsin absorption spectra, but they failed to stimulate the guanosine triphosphatase activity of Gt. The opsin mutations included reversal of a charged pair conserved in all G protein-coupled receptors at the cytoplasmic border of the third transmembrane helix (mutant CD1), replacement of 13 amino acids in the second cytoplasmic loop (mutant CD2), and deletion of 13 amino acids from the third cytoplasmic loop (mutant EF1). Whereas mutant CD1 failed to bind Gt, mutants CD2 and EF1 showed normal Gt binding but failed to release Gt in the presence of guanosine triphosphate. Therefore, it appears that at least the second and third cytoplasmic loops of rhodopsin are required for activation of bound Gt.
Anomaly Detection using Graph Neural Networks (2019)

Conventional methods for anomaly detection include techniques based on clustering, proximity or classification. With the rapidly growing social networks, outliers or anomalies find ingenious ways to obscure themselves in the network and making the conventional techniques inefficient. In this paper, we utilize the ability of Deep Learning over topological characteristics of a social network to detect anomalies in email network and twitter network. We present a model, Graph Neural Network, which is applied on social connection graphs to detect anomalies. The combinations of various social network statistical measures are taken into account to study the graph structure and functioning of the anomalous nodes by employing deep neural networks on it. The hidden layer of the neural network plays an important role in finding the impact of statistical measure combination in anomaly detection.
Metabolic functions of atypical protein kinase C: “good” and “bad” as defined by nutritional status (2009)

Atypical protein kinase C (aPKC) isoforms mediate insulin effects on glucose transport in muscle and adipose tissues and lipid synthesis in liver and support other metabolic processes, expression of enzymes needed for islet insulin secretion and hepatic glucose production/release, CNS appetite suppression, and inflammatory responses. In muscle, selective aPKC deficiency impairs glucose uptake and produces insulin resistance and hyperinsulinemia, which, by activating hepatic aPKC, provokes inordinate increases in lipid synthesis and produces typical "metabolic syndrome" features. In contrast, hepatic aPKC deficiency diminishes lipid synthesis and protects against metabolic syndrome features. Unfortunately, aPKC is deficient in muscle but paradoxically conserved in liver in obesity and type 2 diabetes mellitus; this combination is particularly problematic because it promotes lipid and carbohydrate abnormalities. Accordingly, metabolic effects of aPKCs can be "good" or "bad," depending upon nutritional status; thus, muscle glucose uptake, islet insulin secretion, hepatic glucose and lipid production/release, and adipose fat synthesis/storage would be important for survival during periods of limited food availability and therefore be "good." However, during times of food surfeit, excessive activation of hepatic aPKC, whether caused by overnutrition or impairments in extrahepatic effects of insulin, would lead to inordinate increases in hepatic lipid synthesis and metabolic syndrome features and therefore be "bad." In keeping with these ideas, the inhibition of hepatic aPKC markedly ameliorates lipid and carbohydrate abnormalities in experimental models of obesity and type 2 diabetes. We postulate that a similar approach may be useful for treating humans.
Amoeba: a distributed operating system for the 1990s (1990)

A description is given of the Amoeba distributed operating system, which appears to users as a centralized system but has the speed, fault tolerance, security safeguards, and flexibility required for the 1990s. The Amoeba software is based on objects. Objects are managed by server processes and named using capabilities chosen randomly from a sparse name space. Amoeba has a unique, fast file system split into two parts: the bullet service stores immutable files contiguously on the disk; the directory service gives capabilities symbolic names and handles replication and atomicity, eliminating the need for a separate transaction management system. To bridge the gap with existing systems, Amoeba has a Unix emulation facility consisting of a library of Unix system call routines that make calls to the various Amoeba server processes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors (2013)

One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the eliciting antigen. Advances in technology on several fronts have made it possible to clone large numbers of heavy-chain light-chain pairs from individual B cells and thereby identify whole sets of clonally related antibodies. These collections could provide the information necessary to reconstruct their own history--the sequence of changes introduced into the lineage during the development of the clone--and to study affinity maturation in detail. But the success of such a program depends entirely on accurately inferring the founding ancestor and the other unobserved intermediates. I have developed an Empirical Bayes method that allows one to compute the posterior distribution over ancestors, thereby giving a thorough accounting of the uncertainty inherent in the reconstruction. I demonstrate the application of this method on heavy-chain and light-chain clones, assess the reliability of the inference, and discuss the sources of uncertainty.
Graphs to Prof. Sommerfeld's Attenuation Formula for Radio Waves (1930)

The importance of close confrontation of Prof. Sommerfeld's attenuation formula with field-strength measurements is stressed. The fallacy of Prof. Zenneck's formula in most practical cases is pointed out, and a short summary given of Prof. Sommerfeld's conclusions, with approximate expressions for the "numerical distance" and the angle determining various shapes of theoretical attenuation curves. At very great distances, the signals over flat ground are shown always to decrease as the inverse square of distance, while at short distances short waves die away approximately as the inverse square root of distance. At intermediate distances, curious phenomena are shown to occur; in some cases, as illustrated by examples, the field vanishes altogether at a finite distance, to reappear farther away. An abac is included and instructions given for its use to obtain the inductivity and conductivity of the ground over which a series of field-strength measurements have been made. Results of such computations in Sweden and England are given. By using a graph reproduced in the paper an easy method of predicting field strengths for all wavelengths over soil, whose electrical constants are known, is devised. A simple semi-empirical formula to account for the curvature of the Earth at moderate distances is presented, and lines for better antenna construction touched upon, minimizing jamming from down-coming rays, and saving power as well.
The Role of MR Myelography with Intrathecal Gadolinium in Localization of Spinal CSF Leaks in Patients with Spontaneous Intracranial Hypotension (2011)

GdM is a useful technique in the highly select group of patients who have debilitating symptoms of SIH, a high clinical index of suspicion of spinal CSF leak, and no demonstrated leak on conventional CTM. Intrathecal injection of gadolinium contrast remains an off-label use and should be reserved for those patients who fail conventional CTM.
Determination of the Acoustic Properties of Blood and its Components (1953)

Measurements of absorption and velocity of sound in blood, plasma, and solutions of albumin and hemoglobin have been carried out in the frequency range 800–3000 kc and temperature range 5–45°C. The absorption departs only slightly from a linear dependence upon frequency. Absorption for the various solutions is in direct proportion to protein content. It is concluded that the acoustic properties of blood are largely determined by the proteins which it contains.
Circulating nucleic acids in plasma and serum: diagnosis and prognosis in cancer (2010)

The presence of DNA and RNA circulating in human plasma and serum is described. The known sources of the DNA/RNA in blood, the ability of these nucleic acids to enter other cells and to express in the recipient cells are considered along with their relationship to metastases. The possible role(s) of the DNA/RNA in personalized clinical diagnosis, monitoring of treatment and prognosis in oncology are discussed.
Fetal erythropoiesis in stress hematopoiesis. (1979)

Fetal erythropoiesis occurs during chronic bone marrow failure, or during recovery from marrow suppression. Fetal erythrocytes have HB F, with more G gamma than A gamma chains, "i" antigen, large MCV, characteristic enzyme levels, low carbonic anhydrase, low HB A2, and short life span. Many of these fetal characteristics are present in the red cells of patients with temporary or chronic hematopoietic stress. In those in whom normal hematopoiesis ensues, the fetal erythrocytes disappear. The fetal phase of recovery may be with homologous stem cells after bone marrow engraftment, or with autologous cells. Chronic fetal erythropoiesis is seen in patients with constitutional aplastic anemia, such as Fanconi's anemia or Diamond-Blackfan anemia. In one patient with the latter disorder, fetal erythropoiesis accompanied chronic anemia, and actually decreased slightly during the acute phase of clinical improvement. Culture of late erythroid precursor cells (CFU-Es) from a patient with transient erythroblastopenia of childhood led to in vitro development of colonies with HB F, an event not seen in normal marrow cultures. Thus fetal erythropoiesis occurs during hematopoietic stress, whether chronic or transient, if there is some marrow activity, and may be due to expansion of fetal clones.
Capillary C4d Deposition in Kidney Allografts (2002)

Capillary deposition of the complement split product C4d has been discussed as a marker for antibody-mediated kidney allograft rejection. The relationship between C4d staining and posttransplant alloantibody detection remains to be thoroughly investigated, however. In this study, C4d staining in peritubular capillaries (PTC) and the incidence of alloantibody formation, as detected with sensitive techniques, were evaluated among a cohort of transplant recipients who had undergone biopsies and had not been selected for a specific histologic diagnosis. One hundred thirteen biopsies, obtained from 58 cadaveric kidney transplant recipients, were tested. Serum samples obtained at the time of biopsy were evaluated by flow cytometric crossmatch (FCXM) testing and FlowPRA (One Lambda, Inc., Canoga Park, CA) analysis of anti-HLA panel reactivity. Most biopsies with C4d deposits in PTC (C4d(PTC)(+), n = 21 of 24) were associated with positive posttransplant FCXM results (T and/or B cell FCXM) and/or > or =5% FlowPRA (anti-HLA class I and/or II) reactivity. Approximately 50% of the C4d(PTC)(-) biopsies were observed to be associated with donor-specific alloantibodies. Accordingly, high specificity (93%) but low sensitivity (31%) were calculated for capillary C4d staining (with FCXM testing as the standard method). For clinical evaluation, three patient groups were defined, i.e., a group of recipients with positive C4d staining in at least one allograft biopsy (C4d(PTC)(+), n = 16) and two C4d(PTC)(-) groups, which were discriminated on the basis of posttransplant FCXM results as C4d(PTC)(-)/FCXM(+) (n = 22) and C4d(PTC)(-)/FCXM(-) (n = 20) groups. Univariate analyses revealed significant differences between these groups with respect to serum creatinine levels at 12 mo [median, 2.83 mg/dl (interquartile range, 1.93 to 4.2 mg/dl) versus 1.78 mg/dl (1.47 to 2.24 mg/dl) versus 1.59 mg/dl (1.2 to 1.71 mg/dl), P < 0.001]. Of the five immunologic graft losses, four occurred in the C4d(PTC)(+) group and one occurred in the C4d(PTC)(-)/FCXM(+) group. In a multivariate analysis, C4d positivity was observed to have an independent predictive value for inferior 12-mo graft function (P = 0.02), whereas the observed moderate difference between C4d(PTC)(-)/FCXM(+) and C4d(PTC)(-)/FCXM(-) recipients did not achieve significance. In conclusion, these data demonstrate that positive C4d staining, which is an independent predictor of kidney graft dysfunction, represents a reliable specific marker for antibody-dependent graft injury.
Amplification of the dihydrofolate reductase gene is a mechanism of acquired resistance to methotrexate in patients with acute lymphoblastic leukemia and is correlated with p53 gene mutations (1995)

Although dihydrofolate reductase (DHFR) gene amplification is a common mechanism of resistance to methotrexate (MTX) in tumor cell lines, with the exception of a few case reports, the incidence of this phenomenon as a mechanism of MTX resistance in the clinic has not been reported. We studied 38 untreated patients and 29 patients in relapse with acute lymphoblastic leukemia (ALL) for gene amplification and p53 gene mutations. Three patients were studied both at diagnosis and at each of two relapses after treatment with MTX. Nine of 29 relapsed patients (31%) had low-level DHFR gene amplification (two to four gene copies) associated with increased levels of DHFR mRNA and enzyme activity. Of significance was a correlation of gene amplification with p53 mutations in seven of nine relapsed patients (P < .001). Low-level DHFR gene amplification may be an important cause of MTX resistance in ALL and strengthens the concept that mutations in the p53 gene may lead to gene amplification as a consequence of defective cell cycle control.
Primary human T-cell responses to the major outer membrane protein of Chlamydia trachomatis. (1993)

The major outer membrane protein (MOMP) of Chlamydia trachomatis is the main candidate antigen for a synthetic vaccine against chlamydial infection. Antibodies to surface-exposed epitopes on MOMP neutralize chlamydial infectivity but little is known about T-cell recognition of the molecule. We have measured primary human T-cell responses to recombinant fragments of MOMP as well as to the whole organism and synthetic MOMP peptides. Using antigen-pulsed low density cells (LDC) we were able to stimulate proliferative responses with T cells from most naive individuals. This response was antigen dose dependent and displayed an absolute requirement for dendritic cells in the antigen-presenting cell (APC) population. Several T-cell epitopes were identified in MOMP and one which stimulated T cells from 80% of donors was resolved as a 12 amino acid synthetic peptide. Dual cell surface labelling and cell cycle analysis by FACS revealed that both CD4+ and CD8+ T cells were stimulated in these cultures. The fact that we were able to obtain proliferative responses and interferon-gamma (IFN-gamma) production to MOMP using cells from cord bloods confirmed that these are genuine primary responses. These experiments have identified a region on MOMP, to which T cells from most humans make a primary response, which may be useful in a chlamydial vaccine. The approach is useful for vaccine development in general.
Holographic quarterwave plates (1990)

Quarterwave plates can be made as holographic gratings in positive photoresist. We studied the effect of the grating period and relief depth on the phase retardation and on the rotation of the polarization of the transmitted light. Experiments were performed with gratings of different periods, which also exhibit an antireflection property.
Accurate high-speed liquid handling of very small biological samples. (1993)

Molecular biology techniques require the accurate pipetting of buffers and solutions with volumes in the microliter range. Traditionally, hand-held pipetting devices are used to fulfill these requirements, but many laboratories have also introduced robotic workstations for the handling of liquids. Piston-operated pumps are commonly used in manually as well as automatically operated pipettors. These devices cannot meet the demands for extremely accurate pipetting of very small volumes at the high speed that would be necessary for certain applications (e.g., in sequencing projects with high throughput). In this paper we describe a technique for the accurate microdispensation of biochemically relevant solutions and suspensions with the aid of a piezoelectric transducer. It is suitable for liquids of a viscosity between 0.5 and 500 milliPascals. The obtainable drop sizes range from 5 picoliters to a few nanoliters with up to 10,000 drops per second. Liquids can be dispensed in single or accumulated drops to handle a wide volume range. The system proved to be excellently suitable for the handling of biological samples. It did not show any detectable negative impact on the biological function of dissolved or suspended molecules or particles.
Minocycline Modulation of Alpha-MSH Production by Keratinocytes In vitro (1999)

The anti-inflammatory mechanisms of minocycline, an antibiotic used in the treatment of the inflammatory component of acne, are only partially understood. In addition to inflammation due to cytokines (IL-1, IL-6, TNF-alpha, etc.), recent studies have shown that neuropeptide-mediated neurogenic inflammation may play an important role in cutaneous inflammation. The purpose of this study was to investigate minocycline-induced modulation of cutaneous production of alpha-melanocyte-stimulating hormone (alpha-MSH), a neuropeptide with known anti-inflammatory activity. Two different skin models were used: explants of inflammatory skin and reconstituted skin, both incubated with minocycline at different concentrations and for different time periods. Epidermal production of alpha-MSH, as evaluated by immunofluorescence and immunoperoxidase techniques, showed increased expression in both models. This neuropeptide, which has an anti-inflammatory activity (notably through production of IL-10, antagonism of IL-1 and inhibition of the chemotaxis of polymorphonuclear leukocytes), thus plays a role in the anti-inflammatory action of minocycline.
Preparation of polymandelide by reaction of α‐bromophenylacetic acid and triethylamine (1989)

Abstract Polymandelide was prepared in 77% yield by reaction of α‐bromophenylacetic acid and triethylamine. The product was characterized by 1 H‐ and 13 C‐NMR and IR spectra and isolation and identification of mandelic acid from hydrolysis of the polymer. The NMR spectra indicate the presence of tacticity at CH in the polymer. Molecular weights were determined by GPC and viscosity measurements; n values of 12–20 are comparable to those reported for polymandelides prepared by other methods. The x‐ray powder diffraction pattern showed the product to be completely amorphous. Thermal decomposition was studied using DSC.
Insulin Analogues (2005)

In the 1990s, the value of glycemic control in the management of diabetes became incontrovertible. The interest in producing insulin formulations that are safer than previous formulations and that more closely duplicate the basal and mealtime components of endogenous insulin secretion has yielded insulin analogues with action profiles that afford more flexible treatment regimens and a lower risk of hypoglycemia. This article examines the use of these newer insulins in clinical practice.
5-Fluorouracil derivatives: a patent review (2012)

The search for less toxic 5-FU derivatives, which diminish or circumvent some of its disadvantages, has allowed the development of selective antitumor prodrugs and novel methods for tissue-specific drug delivery. Although some of these oral prodrugs are being used clinically, either alone or in combination therapy with other anticancer agents, it seems that the potential of personalized medicine, including pharmacogenomics and targeted therapy with novel 5-FU derivatives, will improve the management and clinical responses of patients treated with 5-FU-based therapy.
Controlling the Optical Properties of Lemongrass Extract Synthesized Gold Nanotriangles and Potential Application in Infrared-Absorbing Optical Coatings (2005)

Anisotropic metal nanoparticles have distinct optical behavior when compared with their spherical counterparts. In this report, we demonstrate a simple method involving the reduction of aqueous gold ions by the extract of the lemongrass plant leading to the formation of gold nanotriangles with interesting absorption in the near-infrared (NIR) region of the electromagnetic spectrum. We show that, by simple variation of the experimental conditions, it is possible to vary the size of the gold nanotriangles and, thus, to tune the absorbance of flat gold nanoparticles in the NIR region. The NIR absorption of the gold nanotriangles is expected to be of application in hyperthermia of cancer cells and in IR-absorbing optical coatings. We show that the lemongrass extract synthesized gold nanotriangles can be easily cast in the form of films on glass substrates and that these films are highly efficient in absorbing IR radiation for potential architectural applications.
Long-term effect of interferon alpha alone or after prednisone withdrawal in chronic hepatitis B. Interim report and review of the literature. (1996)

In spite of the few number of cases studied, these results could indicate an improved long-term evolution after a short course of steroids prior to Interferon in selected chronic hepatitis B patients.
Streptococcus Agalactiae Gene And Gene Product Variations (1997)

Streptococcus agalactiae (group B streptococci; GBS) are serotyped on the basis of the capsular polysaccharide antigens and subtyped on the basis of the strain-variable and surface-localised c proteins c alpha, c beta, and R proteins. This study compared c beta protein detection and the polymerase chain reaction (PCR) for beta gene detection, by examining 50 clinical GBS strains. The c beta protein was detected by antibody-based immunofluorescence in a GBS whole-cell assay and Western blotting by probing with the anti-c beta antibody or human IgA. Absorption experiments were performed to test for surface-anchoring of c beta; and bacterial supernates were examined to test for c beta production. Primers for the PCR target regions resulted in a 620-bp product that included beta gene-encoding IgA-binding domains. The results demonstrated four categories of GBS with respect to the beta gene and the c beta protein: (1) strains (16 of 50) that harboured the beta gene and regularly expressed normal surface-localised c beta with a M(r) of 120 kDa; (2) strains (5 of 50) that harboured the gene but did not express the protein; (3) strains (2 of 50) that harboured the gene but expressed a c beta that was not surface-localised and had reduced M(r); (4) strains (27 of 50) without beta gene and c beta expression. One strain amongst the third group generated a PCR product of 1330 bp. These results demonstrate considerable strain variability of the beta gene of GBS and of its product the c beta protein.