gebhart/patrepeval huggingface dataset:
HIV-1 Neutralizing Antibodies Display Dual Recognition of the Primary and Coreceptor Binding Sites and Preferential Binding to Fully Cleaved Envelope Glycoproteins (2012)

The gp120 CD4 binding site (CD4bs) and coreceptor binding site (CoRbs) are two functionally conserved elements of the HIV-1 envelope glycoproteins (Env). We previously defined the presence of CD4bs-neutralizing antibodies in the serum of an HIV-1-infected individual and subsequently isolated the CD4bs-specific monoclonal antibodies (MAbs) VRC01 and VRC03 from the memory B cell population. Since this donor's serum also appeared to contain neutralizing antibodies to the CoRbs, we employed a differential fluorescence-activated cell sorter (FACS)-based sorting strategy using an Env trimer possessing a CoRbs knockout mutation (I420R) to isolate specific B cells. The MAb VRC06 was recovered from these cells, and its genetic sequence allowed us to identify a clonal relative termed VRC06b, which was isolated from a prior cell sort using a resurfaced core gp120 probe and its cognate CD4bs knockout mutant. VRC06 and VRC06b neutralized 22% and 44% of viruses tested, respectively. Epitope mapping studies revealed that the two MAbs were sensitive to mutations in both the gp120 CoRbs and the CD4bs and could cross-block binding of both CD4bs and CoRbs MAbs to gp120. Fine mapping indicated contacts within the gp120 bridging sheet and the base of the third major variable region (V3), which are elements of the CoRbs. Cell surface binding assays demonstrated preferential recognition of fully cleaved Env trimers over uncleaved trimers. Thus, VRC06 and VRC06b are Env trimer precursor cleavage-sensitive neutralizing MAbs that bind to a region of gp120 that overlaps both the primary and the secondary HIV-1 receptor binding sites.
Effects of exogenous melatonin on human pituitary and adrenal secretions. Hormonal responses to specific stimuli after acute administration of different doses at two opposite circadian stages in men. (1989)

We evaluated the effect of an acute oral administration of 2 dosages (100 and 1 mg) of melatonin (MT) vs placebo (PL) on pituitary release of LH, FSH, TSH and PRL after GnRH + TRH and on the adrenocortical release of cortisol, aldosterone and progesterone after ACTH in healthy adult males. We carried out a double blind study on 6 volunteers in winter-early spring, at 2 opposite phases of the circadian cycle: 08(00) and 20(00). Injection of GnRH (100 micrograms), TRH (200 micrograms) and ACTH (10 micrograms of the synthetic analogue ACTH 1-17, alsactide) was performed 1 h after MT or PL ingestion. The measurement of plasma MT levels confirmed its effective gastrointestinal absorption after both doses. The hormonal patterns were superimposable after MT and PL. A higher response of FSH, PRL, cortisol and aldosterone was observed in the evening vs morning protocols independently of previous treatment (MT or PL). Our data demonstrate that the acute oral administration of 2 different doses of MT at 2 opposite circadian stages is ineffective as to the modification of a variety of pituitary and adrenocortical responses in human male subjects. The circadian chronosusceptibility of pituitary and adrenocortical cells to specific stimuli deserves interest to future investigation.
A New Subtype of Large B-Cell Lymphoma Expressing the ALK Kinase and Lacking the 2; 5 Translocation (1997)

Seven cases of large B-cell lymphoma which define a previously unrecognized subgroup are reported. Morphologically they are comprised of monomorphic large immunoblast-like cells, containing large central nucleoli, which tend to invade lymphatic sinuses. Superficially they resemble anaplastic large cell lymphoma (ALCL) but they lack CD30. These lymphomas express epithelial membrane antigen (as do ALCL), but also contain intracytoplasmic IgA of a single light chain type (five cases) and an endoplasmic reticulum-associated marker detected by antibody VS38. They lack lineage-associated leukocyte antigens with the exception of CD4 (5 of 5 cases) and CD57 (5 of 7 cases). They are labeled by antibodies detecting both the intracytoplasmic and extracellular regions of the ALK receptor kinase, suggesting that they express the full-length form of this molecule. This was confirmed by Western blotting (in the one case tested) which showed a band of 200 kD in tumor cell lysates, and by polymerase chain reaction (PCR) amplification of mRNA encoding intracellular and extracellular ALK sequences (in the two cases tested). There was no evidence by cytogenetics (one case analyzed) or reverse transcriptase-PCR (three cases tested) of the 2; 5 translocation or the resultant NPM-ALK gene, as is commonly found in ALCL. All but one of the patients were male and all but one were adults, and in all but the latter case the disease followed an aggressive course.
Mac-1 (CD11b/CD18) and the urokinase receptor (CD87) form a functional unit on monocytic cells (1996)

The leukocyte integrin Mac-1 (CD11b/CD18) and the urokinase receptor (uPAR, CD87) mediate complementary functions in myelomonocytic cells. Both receptors promote degradation of fibrin(ogen) and also confer adhesive properties on cells because Mac-1 and uPAR bind fibrin and vitronectin, respectively. Staining of lung biopsy specimens from patients with acute lung injury indicated that fibrin and vitronectin colocalize at exudative sites in which macrophages bearing these receptors accumulate. Because of the parallel roles and physical proximity of Mac-1 and uPAR, the capacity of these receptors to functionally interact was explored. Induction of Mac-1 and uPAR expression on monocytic cell lines by transforming growth factor- beta 1 and 1.25-(OH)2 vitamin D3 conferred urokinase and uPAR-dependent adhesion to vitronectin, which was further promoted by engagement of Mac-1. Vitronectin attachment promoted subsequent Mac-1-mediated fibrinogen degradation threefold to fourfold. In contrast, enhancement of uPAR occupancy by exogenous urokinase or receptor binding fragments thereof inhibited Mac-1 function. Addition of urokinase progressively inhibited Mac-1-mediated fibrinogen binding and degradation (maximal inhibition, 91% +/- 14% and 72% +/- 15%, respectively). Saturation of uPAR with urokinase also inhibited binding of the procoagulant Mac-1 ligand, Factor X. These inhibitory effects of uPAR were reproduced in fresh monocytes, cultured monocytic cells, and in Chinese hamster ovary (CHO) cells transfected with both human Mac-1 and human uPAR. These data show that the procoagulant and fibrinolytic potential of monocytic cells is co-ordinately regulated by ligand binding to both Mac-1 and uPAR and identify uPAR as a regulator of integrin function. Vitronectin-enhanced fibrin(ogen) turnover by Mac-1 may operate as a salvage pathway in the setting of urokinase and plasmin inhibitors to promote clearance of the provisional matrix and subsequent healing.
Comparative bioavailability of ferric polymaltose and ferrous sulphate in iron‐deficient blood donors (1993)

Absolute iron deficiency is treated by correcting the causative lesion and then, traditionally, administering sufficient amounts of ferrous salt to return the haemoglobin level to normal and replenish body stores. The bioavailability of ferric compounds has been questioned and accordingly their therapeutic role remains controversial. A special problem is posed by regular blood donation, where the frequency of phlebotomy is limited by the haemoglobin level, which, in turn, requires maintenance of an adequate supply of iron from dietary sources. Since this latter situation may not always occur, it would be of practical benefit to have a form of supplementation that is effective and can be taken without side effects. These issues were prospectively examined in a consecutive series of otherwise healthy blood donors who developed absolute iron deficiency anaemia and were then randomly allocated to receive 60 mg of this metal as ferrous sulphate twice a day (Group 1: n = 51), 100 mg as chewable ferric polymaltose daily (Group 2: n = 53), or the latter product twice a day (Group 3: n = 55). Serial studies showed that 80% of patients in Groups 1 and 3 had reached normal haemoglobin levels by 12 weeks, but this figure was only 50% in Group 2. Similarly, the proportion of patients improving their percentage saturation of transferrin to within the normal range was significantly better in Groups 1 and 3 than in Group 2 (P < .01). However, body iron stores, reflected in serum ferritin level, was significantly better in Group 1 (P < .01); there was no difference in this respect between Groups 2 and 3.(ABSTRACT TRUNCATED AT 250 WORDS)
Small-Conductance, Calcium-Activated Potassium Channels from Mammalian Brain (1996)

Members of a previously unidentified family of potassium channel subunits were cloned from rat and human brain. The messenger RNAs encoding these subunits were widely expressed in brain with distinct yet overlapping patterns, as well as in several peripheral tissues. Expression of the messenger RNAs in Xenopus oocytes resulted in calcium-activated, voltage-independent potassium channels. The channels that formed from the various subunits displayed differential sensitivity to apamin and tubocurare. The distribution, function, and pharmacology of these channels are consistent with the SK class of small-conductance, calcium-activated potassium channels, which contribute to the afterhyperpolarization in central neurons and other cell types.
Specificity of the binding domain of glucoamylase 1 (1993)

Glucoamylase 1 from Aspergillus niger hydrolyses granular starch at an increased rate due to the presence of a C-terminal starch-binding domain. This domain was isolated and shown to bind to the malto-oligosaccharides Glc2 to Glc11 with a stoichiometry of 1 mol ligand/mol protein. The affinity for these ligands increased with increasing degree of polymerisation until Glc9, above which no further increase was observed. We suggest that this indicates that for maximum affinity the substrate should be able to form a helical conformation, which mimics the conformation of amylose in granular starch. We propose a model of how the complex between the malto-oligosaccharides and the binding domain is formed and indicate how this affects the differences in binding modes for soluble and insoluble substrates. Glucono-1,5-lactone interacts with the binding domain at a different site to the malto-oligosaccharides allowing the formation of a ternary complex between the binding domain, a malto-oligosaccharide and glucono-1,5-lactone. The binding domain also binds to linear alpha-1,6-linked glucose digosaccharides (dextran), but with much lower affinity than for alpha-1,4-linked glucose. This ligand appears to interact with the binding domain at both binding sites, i.e. at the site to which the malto-oligosaccharides bind and also at the site to which glucono-1,5-lactone binds. The relevance of the results to the mechanism of action of other polysaccharide-hydrolysing enzymes containing both a catalytic and a binding domain is discussed.
Insulin-Resistant Diabetes Due to a Point Mutation That Prevents Insulin Proreceptor Processing (1988)

A point mutation in the human insulin receptor gene in a patient with type A insulin resistance alters the amino acid sequence within the tetrabasic processing site of the proreceptor molecule from Arg-Lys-Arg-Arg to Arg-Lys-Arg-Ser. Epstein-Barr virus-transformed lymphocytes from this patient synthesize an insulin receptor precursor that is normally glycosylated and inserted into the plasma membrane but is not cleaved to mature alpha and beta subunits. Insulin binding to these cells is severely reduced but can be increased about fivefold by gentle treatment with trypsin, accompanied by the appearance of normal alpha subunits. These results indicate that proteolysis of the proreceptor is necessary for its normal full insulin-binding sensitivity and signal-transducing activity and that a cellular protease that is more stringent in its specificity than trypsin is required to process the receptor precursor.
Metal-Catalyzed Coupling Reactions on an Olefin Template:  The Total Synthesis of (13E,15E,18Z,20Z)-1-Hydroxypentacosa- 13,15,18,20-tetraen-11-yn-4-one 1-Acetate (2004)

The naturally occurring ant venom (13E,15E,18Z,20Z)-1-hydroxypentacosa-13,15,18,20-tetraen-11-yn-4-one 1-acetate was synthesized stereospecifically using a series of metal-mediated cross-coupling reactions. The use of the difunctional olefin template (E)-1-chloro-2-iodoethylene as the central, pseudosymmetrical building block facilitated a fully convergent and, thus, efficient strategy to prepare this polyunsaturated natural product.
Loss of basement membrane components by invasive tumors but not by their benign counterparts. (1983)

Highly purified antibodies to two ubiquitous components of basement membrane, type IV collagen and laminin, were applied to both fresh-frozen and formalin-fixed tissue sections of a variety of invasive carcinomas, carcinomas in situ, and their "look-alike" benign counterparts. These included lesions of the breast (infiltrating ductal carcinoma, comedocarcinoma, and sclerosing adenosis); lesions of the skin (squamous cell carcinoma, Bowen's disease, and pseudoepitheliomatous hyperplasia); lesions of the pancreas (adenocarcinoma and pancreatitis); lesions of the prostate (adenocarcinoma and benign prostatic hyperplasia); and other epithelial lesions of the invasive, in situ, and benign category. By both immunofluorescence and immunoperoxidase techniques, benign and in situ lesions showed intact basement membranes with linear staining of type IV collagen and laminin. The majority of invasive carcinomas, in contrast, lacked immunoreactivity for both of these basement membrane components. In cases of in situ carcinoma with microinvasion, there was thinning, fragmentation, and disruption of the basement membrane in the foci of microinvasion but not elsewhere. Utilizing antibodies to type IV collagen and laminin aids in both understanding the pathophysiology of the invasive process and the recognition of its presence in tissue sections.
Development of low temperature bonding using in-based solders (2008)

In-based solders were chosen for the low temperature bonding at lower than 180degC. Three kinds of bonding types on Au/Cu/Ti/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si dies, which were Sn/In and Au/In for Type 1, Au/In and Au/Sn for Type 2, and InSn alloy and InSn alloy for Type 3, were studied expecting that the whole In- solder layer is converted to the mixed intermetallic compound (IMC) phases of In-Cu and In-Au IMCs after bonding below 180degC and annealing at 100~120degC. The IMC in the joints were characterized in terms of the micro structure observations and the compositional analysis with Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDX), the phase identification with X-ray Diffraction (XRD) and the re-melting temperature with Differential Scanning Calorimetry (DSC). The phase equilibriums of the joints were examined by thermodynamic calculations to understand the re-melting behavior. As a result, complete bonding consisted of only high melting temperature IMCs, Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> ln <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sub> , Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> In, eta-Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> , and Auln <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , was successfully made at 120degC followed by annealing at 100degC in Type 3, and at 160degC with annealing for lOhrs or at 180degC without annealing for Type 1, which was confirmed by DSC measurements and explained through thermodynamic calculations.
On achievable rates in a multi-antenna Gaussian broadcast channel (2002)

A Gaussian broadcast channel with r single-antenna receivers and t antennas at the transmitter is considered. Both transmitter and receivers have perfect knowledge of the channel. Despite its apparent simplicity, this model is in general a non-degraded broadcast channel, for which the capacity region is not fully known. We propose a novel transmission scheme based on "ranked known interference" (RKI). In brief, the transmitter decomposes the channel into an ordered (or ranked) set of interference channels for which the interference signal of the i-th channel is generated as a linear combination of the signals transmitted in channels j<i. In this way, known techniques of coding for non-causally known interference can be applied to make the interference in each channel harmless without further power penalty. We show that the proposed scheme is throughputwise asymptotically optimal for both low and high SNR. We provide a modification of the basic RKI scheme which achieves optimal throughput for all SNRs in the special case of 2 antenna and 2 users. For independent Rayleigh fading closed-form throughput expressions are obtained in various cases of interest and numerical examples are provided for the infinite-dimensional Rayleigh channel.
Polarization effects in mask transmission (1992)

Polarization and interface reflection effects are examined for technology issues in mask making of chrome edge shape, overcoating, double phase-shifting removal of defects, and reflective masks. This study is based on the massively parallel rigorous electromagnetic simulator TEMPEST1, with extensions to include the TM polarization and boundary conditions for outgoing waves in optical materials. The analysis was carried out on a CM-2 connection machine with remote electronic access. A local workstation was used to write and preview the geometry as well as process images from files of diffraction efficiencies downloaded to the workstation from the network. Through this remote analysis procedure, the four proto-typical mask case studies described by Doi et al.2 were examined for polarization and boundary condition effects. For chrome masks of one wavelength wide opening in a IX system at 0.248 |im, moderate differences between the TE and the TM polarizations were observed in the peak intensities (10%). The TM polarization in general showed higher transmission and lower sidelobes. The two polarizations showed a similar increase in linewidth and peak intensity with decreasing chrome edge slope. The difference was not as pronounced for a 5X system at 0.365 |Lim. Overcoating chrome masks with anti-reflection layers improved resolution for both polarizations. For 5X chromeless phase-shifting masks at 0.365 pm, neither polarization effect nor phase-shifter edge slope was important. The peak intensity at the phase-shifting section changed by only 1% and the linewidth varied by less than 2% when the phase-shifter edge slope changed from 90° to 45°, keeping the mid-points of the phase-shifter edge fixed. To remove defects on such masks by double phase-shifting may drop the intensity level to 70% of the clear field value for a 0.1 X/NA sized defect. For IX reflective masks at one wavelength, both polarizations displayed similar behaviors. These reflective masks with built-in material-based phase-shifting improved the image slope, and the TM polarization was found to have slightly less ringing than the TE polarization.
Differential Expression of Class I Major Histocompatibility Complex Determinants by Lymphoblastic Leukemia- Lymphoma Cell Lines (1990)

Two T-cell lines (XR11-4T and XR11-5T), established from radiation-induced, murine lymphoblastic lymphomas, were examined for the expression of class I major histocompatibility complex antigen and tumor induction. These cell lines expressed class I private determinants, H-2.9 and H-2.26, but not the monomorphic determinant defined by monoclonal antibody M1/42. Both cell lines produced tumors in syngeneic and allogeneic hosts. The monomorphic determinant could be demonstrated on both cell lines following growth in allogeneic (BALB/c mice) but not in syngeneic (RFM mice) hosts. The re-expressed determinant present on cells following growth in allogeneic mice was not of host origin. Thus, tumorigenic x irradiation may differentially affect the expression of class I major histocompatibility complex determinants.
Forging a field: the golden age of iron biology (2008)

Oh what a difference a decade makes! In a landmark paper published in 1996, Feder and colleagues identified the long-sought gene mutated in patients with classical hereditary hemochromatosis. In many ways, this seemed to ignite an explosion in iron biology which, over the next 10 years, led to a
Radio Channel Characterization in Industrial Environments and Spread Spectrum Modem Performance (2006)

In this work the characteristics of the radio channel of a typical industrial environment are examined in detail by means of experimental measurements. The channel impulse response is measured at several representative positions. These measurements are then used to calculate important propagation parameters like attenuation, rms delay spread and coherence bandwidth. Furthermore, directional antennas are used to investigate the effect of directional transmission in propagation parameters. Finally, the performance of direct sequence spread spectrum (DSSS) radio transmission (in the 2.4 GHz band) is evaluated for omnidirectional and directional reception by means of bit error rate (BER) measurements at the same characterized positions
Comparison of octreotide acetate LAR and lanreotide SR in patients with acromegaly (2000)

Octreotide LAR 20 mg administered once monthly was more effective than lanreotide SR 30 mg administered 2 or 3 times monthly in reducing GH and IGF-I in patients with acromegaly.
Chemical modifications and bioconjugate reactions of nanomaterials for sensing, imaging, drug delivery and therapy (2013)

As prepared nanomaterials of metals, semiconductors, polymers and carbon often need surface modifications such as ligand exchange, and chemical and bioconjugate reactions for various biosensor, bioanalytical, bioimaging, drug delivery and therapeutic applications. Such surface modifications help us to control the physico-chemical, toxicological and pharmacological properties of nanomaterials. Furthermore, introduction of various reactive functional groups on the surface of nanomaterials allows us to conjugate a spectrum of contrast agents, antibodies, peptides, ligands, drugs and genes, and construct multifunctional and hybrid nanomaterials for the targeted imaging and treatment of cancers. This tutorial review is intended to provide an introduction to newcomers about how chemical and bioconjugate reactions transform the surface of nanomaterials such as silica nanoparticles, gold nanoparticles, gold quantum clusters, semiconductor quantum dots, carbon nanotubes, fullerene and graphene, and accordingly formulate them for applications such as biosensing, bioimaging, drug and gene delivery, chemotherapy, photodynamic therapy and photothermal therapy. Nonetheless, controversial reports and our growing concerns about toxicity and pharmacokinetics of nanomaterials suggest the need for not only rigorous in vivo experiments in animal models but also novel nanomaterials for practical applications in the clinical settings. Further reading of original and review articles cited herein is necessary to buildup in-depth knowledge about the chemistry, bioconjugate chemistry and biological applications of individual nanomaterials.
THREE DIMENSIONAL STRUCTURE OF HUMAN HBP/CAP37/AZUROCIDIN. (1997)

Dept. of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark.