gebhart/patrepeval huggingface dataset:
Bovine IgG repertoire is dominated by a single diversified VH gene family (1997)

Using methods based upon the PCR, we have analyzed sequences that encode the V domain of bovine Ig heavy chain. Pairwise comparison indicates that the heavy chain repertoire in cattle is dominated by a single VH gene family that is homologous to human VHII. The third complementarity-determining region (CDR3) is particularly variable and 60% of the sequences encode a CDR3 in excess of 21 amino acids. Southern blots, single-stranded conformation polymorphism analysis, and sequencing of segments from the germline indicate that the dominant VHII gene family is of small size, comprising as few as 10 unique members, and carries a very low level of diversity in CDRs 1 and 2. Comparison of germline VH sequences with those gathered from adult bovine splenic cDNA demonstrates a pattern of nucleotide substitution that is consistent with diversification through somatic hypermutation.
A New Species Of The Genus Platymantis (Amphibia: Ranidae) From Luzon Island, Philippines (1997)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
The Functional Assessment of Cancer Therapy-Anemia (FACT-An) Scale: a new tool for the assessment of outcomes in cancer anemia and fatigue. (1997)

Anemia, frequently associated with cancer and cancer treatment, can use a variety of symptoms that diminish overall quality of life (QOL). Fatigue is the most commonly reported symptom among cancer patients and can significantly affect their daily lives. Using the Functional Assessment of Cancer Therapy-General (FACT-G) instrument, which measures general QOL, as a core questionnaire, 20 new questions related to the impact of fatigue and other anemia-related symptoms on patients with cancer were developed. Two new instruments were produced: the FACT-Fatigue (FACT-F), consisting of the FACT-G plus 13 fatigue items (the Fatigue Subscale), and the FACT-Anemia (FACT-An), consisting of the FACT-F plus seven items addressing other concerns related to anemia, but unrelated to fatigue. FACT-F and FACT-An demonstrated good stability (r = .87 for both) and strong internal consistency (alpha = .95 and .96, respectively). Test-retest reliability coefficients for the Fatigue Subscale and nonfatigue items also showed good stability (r = .84 to .90), and the Fatigue Subscale showed strong internal consistency (alpha = .93 to .95). Convergent and discriminant validity testing revealed a significantly positive relationship with other known measures of fatigue, a significant negative relationship with vigor, and an anticipated lack of relationship with social desirability. The FACT-An, FACT-F, and Fatigue Subscale were found to successfully discriminate patients based on hemoglobin (Hb) level and Eastern Cooperative Oncology Group (ECOG) performance status. When patients were divided into two groups by Hb levels, patients with Hb levels greater than 12 g/dL reported significantly less fatigue, fewer nonfatigue anemia symptoms, better physical well-being, better functional well-being, and higher general QOL. The FACT-An, the FACT-F, and the Fatigue Subscale are useful measures of QOL in cancer patients and add focus to the widespread clinical problems of anemia and fatigue.
Tissue-specific induction of CCR6 and Nrp1 during early CD4+ T cell differentiation (2016)

Upon differentiation, T cells acquire tissue-specific homing properties allowing efficient targeting of effector T cells into distinct inflamed organs. Priming of T cells within skin-draining, peripheral lymph nodes (pLNs) leads to the expression of E- and P-selectin ligands, which facilitate migration into inflamed skin, whereas activation within gut-draining, mesenteric LNs (mLNs) results in induction of chemokine receptor CCR9 and integrin α<sub>4</sub>β<sub>7</sub>, both required for migration of effector T cells into mucosal tissues. In addition to the local tissue microenvironment, both organ-specific dendritic cells and LN-resident stromal cells are critical factors to shape T cell migration properties. Here, we identify two additional homing-related molecules, CCR6 and Neuropilin-1 (Nrp1), upregulated in T cells early during differentiation solely in pLNs, but not mLNs. Surprisingly, intestinal inflammation resulted in an ameliorated induction of CCR6 and Nrp1 in pLNs, suggesting that a local inflammation within the gut can systemically alter T cell differentiation. Finally, transplantation of mLNs to a skin-draining environment revealed that LN stromal cells also contribute to efficient CCR6 induction in pLNs. Collectively, these findings identify further aspects of early T cell differentiation within skin-draining pLNs, which could be utilized to further develop tailored and highly specialized vaccination strategies.
Standing surface acoustic wave (SSAW) based multichannel cell sorting (2012)

We introduce a novel microfluidic device for cell sorting in continuous flow using tunable standing surface acoustic waves. This method allows individual cells to be precisely directed into five different outlet channels in a single step. It is versatile, simple, label-free, non-invasive, and highly controllable.
Characterization of High Density Lipoprotein-Bound and Soluble RT6 Released Following Administration of Anti-RT6.1 Monoclonal Antibody (1998)

RT6 is a rat lymphocyte glycosylphosphatidylinositol (GPI)-anchored alloantigen with nicotinamide adenine dinucleotide (NAD) glycohydrolase (NADase) and auto-ADP-ribosyltransferase activities. RT6 may have immunoregulatory properties based in part on the observation that injection of diabetes-resistant (DR)-BB rats with depleting doses of anti-RT6.1 mAb induced autoimmune diabetes and thyroiditis. We now report that injection of DR-BB rats with anti-RT6.1 mAb increased plasma NADase activity, which localized, by fluid phase liquid chromatography fractionation, to the high density lipoprotein (HDL) fraction. Following ultracentrifugation in high salt, however, RT6 was found in the nonlipoprotein fraction, where it existed, under nondenaturing conditions, as a 200-kDa complex and, by SDS-PAGE, as a 30- to 36-kDa species. Thy-1, another GPI-linked protein, and proteins that reacted with anti-GPI-oligosaccharide Abs also translocated from HDL to the nonlipoprotein fraction under similar conditions. Injection of anti-RT6.1 mAb into thymectomized DR and diabetes-prone-BB rats increased soluble RT6 to levels comparable to those observed in euthymic DR-BB rats, suggesting that HDL-bound RT6 is not derived from peripheral lymphocytes. In agreement, NADase activity in the plasma of eviscerated DR-BB rats did not increase following injection of anti-RT6 mAb. These data suggest that HDL is a carrier of plasma RT6 and other GPI-linked proteins, with equilibrium between the lipoprotein and nonlipoprotein fractions being salt dependent. Since GPI-linked proteins in HDL can transfer to cells in a functionally active form, the presence of RT6 in HDL is consistent with it having a role in signaling in nonlymphoid cells.
The use of virus-like particles for gene transfer. (2003)

A major challenge in the field of gene therapy is the development of new carrier/delivery systems that lack the disadvantages of current transfer systems. In the past, some time has been spent developing such modified or alternative vectors. A new candidate is represented by virus-like particles (VLPs). It has been shown that recombinant expression of the major structural proteins of many viruses leads to the formation of VLPs. Such VLPs exhibit morphology similar to the empty capsids of the virus from which they are derived. VLPs are non-infectious, have a similar tropism to the natural virus, and show comparable cellular uptake and intracellular trafficking. Since its discovery, VLP technology has gained importance in biomedical research. Although most investigations into VLP technology have dealt with vaccine development, some research groups have demonstrated that VLPs could also represent a useful gene therapy delivery system. This review will focus on studies performed with VLPs from members of the Papillomaviridae and Polyomaviridae families.
Molecular cloning of the mouse polymeric Ig receptor. Functional regions of the molecule are conserved among five mammalian species. (1995)

Transcytosis of polymeric Ig (pIg) by mucosal epithelial cells is mediated by the polymeric Ig receptor (pIgR). Here we describe the characterization of a 3095-bp mouse pIgR cDNA, which encodes a protein of 771 amino acids. Northern blot analysis detected a single mouse pIgR transcript of 3.9 kb, expressed at high levels in small intestine and liver, and at low levels in lung. Alignment of the amino acid sequences of mouse, rat, human, bovine, and rabbit pIgR revealed that functional regions of the molecule are conserved across species. In the extracellular region, conserved motifs include: a 23-amino acid pIg-binding site, 11 intradomain disulfide bonds, consensus sites for N-glycosylation, and a putative cleavage site at which the extracellular region of pIgR (secretory component) is released from the plasma membrane. A 10-amino acid sequence within the transmembrane region is highly conserved, possibly reflecting a mechanism for transmitting signals from the extracellular region to the cytoplasmic tail. Conservation within the cytoplasmic tail of pIgR is clustered in motifs that mediate polarized sorting, endocytosis, and transcytosis.
Peptide–membrane interactions and a new principle in quantitative structure–activity relationships (1991)

Abstract Ideas about “active conformations” of peptides as the basis of their biological action are reviewed and put into perspective with recent work on the possible role of the lipid phase of the target cell membrane in mediating receptor subtype selectivity.
Harmonics-based multiple heartbeat detection at equal distance using UWB impulse radar (2018)

In this paper, we discuss and demonstrate the possibility of detecting multiple heartbeat of stationary subjects at equal distance away from a single input and single output UWB radar. To that end, we propose a novel concept to extract the heartbeat information from its harmonics to deal with the spurious peaks of respiration signal and intermodulations between respiration and heartbeat signals. We provide a numerical analysis to justify the proposed algorithm. We compare the ability of suppressing the interferencing harmonics between the proposed algorithm and other detection algorithms. Finally, we provide an experimental example and show that accurate heart rates detection from two subjects at equal distance can be achieved using the proposed method by comparing against two types of references: camera based system and chest heart rate sensor.
Convenient and direct preparation of tertiary phosphines via nickel-catalysed cross-coupling (1997)

Nickel-catalysed cross-coupling of aryl sulfonates and aryl halides with chlorodiphenylphosphine and a reductant directly affords tertiary phosphines, which have application in a wide variety of asymmetric catalysis.
Soluble complement receptor one (sCR1) inhibits the development and progression of rat collagen-induced arthritis (2000)

We set out to determine whether inhibition of complement using sCR1 could influence the development and progression of collagen arthritis in the Lewis rat. Collagen arthritis was successfully established in the Lewis rat, using a novel immunization schedule. In separate experiments, cobra venom factor (CVF) and sCR1 were used to achieve systemic complement inhibition. Their respective effects on disease onset and on the progression of established disease compared with saline-treated control animals was explored. Arthritis was assessed by measurement of clinical score, paw diameter and paw volume. Complement inhibition using either CVF or sCR1, prior to the onset of clinical signs of inflammation, delayed the development of disease. CVF was ineffective in the treatment of established disease, whereas sCR1 delayed the progression of disease in affected joints and prevented the recruitment of further joints while the animals were complement-depleted. In the control saline-treated groups the disease continued to progress relentlessly. We conclude that complement activation is important in the initiation and maintenance of inflammation in collagen arthritis. The potent disease-modulating effect of sCR1 provides persuasive evidence that specific complement inhibiting agents may be an effective approach to the treatment of inflammatory joint diseases
Diagnosis and symptomatic treatment of migraine. (1997)

Migraine is a common, complex neurophysiologic headache disorder. Most migraineurs have neither been diagnosed by physicians nor effectively treated. The clinical diagnosis of migraine is based on headache characteristics and associated symptoms, particularly nausea and vomiting. Pharmacologic symptomatic treatment is aimed at reversing, aborting, or reducing pain and the accompanying symptoms of an attack. Individualization of therapy is essential in determining whether symptomatic and/or preventive treatment for migraine attacks are needed. The presence of nausea and vomiting must be considered in developing a treatment plan. The patient's priorities and preferences regarding therapy must be taken into account. The goals of symptomatic treatment are to relieve pain and the associated symptoms and to optimize the patient's ability to function normally. Multiple treatment strategies utilizing combinations of 5-hydroxytryptamine1 (5-HT1) agonists (ergotamine tartrate [ET], sumatriptan, and dihydroergotamine [DHE]) with simple analgesics, nonsteroidal anti-inflammatory drugs (NSAIDs), and opiates provide effective treatment for most attacks of moderate to severe migraine. Treatment strategies are based on the frequency, nature, and severity of attacks. Patients with intractable, acute migraine may require hospitalization and aggressive parenteral treatment. Wider use of currently available diagnostic criteria and symptomatic medications should improve the diagnosis and treatment of migraine.
The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins. (1987)

Ricin is a potent cytotoxic protein derived from the higher plant Ricinus communis that inactivates eukaryotic ribosomes. In this paper we have studied the mechanism of action of ricin A-chain on rat liver ribosomes in vitro. Our findings indicate that the toxin inactivates the ribosomes by modifying both or either of two nucleoside residues, G4323 and A4324, in 28 S rRNA. These nucleotides are located close to the alpha-sarcin cleavage site and become resistant to all ribonucleases tested. The examination of the lability of phosphodiester bonds of these nucleotides to both mild alkaline digestion and aniline treatment at acidic pH suggests that the base of A4324 is removed by the toxin. This unique activity of ricin A-chain was also observed when naked 28 S rRNA is used as a substrate, indicating that the toxin directly acts on the RNA. Similar activity on 28 S rRNA is also exhibited by abrin and modeccin, ricin-related toxins, suggesting a general mechanistic pathway for ribosome inactivation by lectin toxins.
Facile synthesis of enzyme–inorganic hybrid nanoflowers and their application as an immobilized trypsin reactor for highly efficient protein digestion (2014)

Hybrid nanoflowers were synthesized by a novel approach. The nanoflowers exhibited an enhanced enzymatic activity and can be used as an immobilized enzyme reactor (IMER) for highly efficient protein digestion.
Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. (1997)

We have designed a self-cleaving ribozyme construct that is rendered inactive during preparative in vitro transcription by allosteric interactions with ATP. This allosteric ribozyme was constructed by joining a hammerhead domain to an ATP-binding RNA aptamer, thereby creating a ribozyme whose catalytic rate can be controlled by ATP. Upon purification by PAGE, the engineered ribozyme undergoes rapid self-cleavage when incubated in the absence of ATP. This strategy of "allosteric delay" was used to prepare intact hammerhead ribozymes that would otherwise self-destruct during transcription. Using a similar strategy, we have prepared a combinatorial pool of RNA in order to assess the catalytic fitness of ribozymes that carry the natural consensus sequence for the hammerhead. Using in vitro selection, this comprehensive RNA pool was screened for sequence variants of the hammerhead ribozyme that also display catalytic activity. We find that sequences that comprise the core of naturally occurring hammerhead dominate the population of selected RNAs, indicating that the natural consensus sequence of this ribozyme is optimal for catalytic function.
Separated Metallic and Semiconducting Single-Walled Carbon Nanotubes: Opportunities in Transparent Electrodes and Beyond (2010)

Ever since the discovery of single-walled carbon nanotubes (SWNTs), there have been many reports and predictions on their superior properties for use in a wide variety of potential applications. However, an SWNT is either metallic or semiconducting; these properties are distinctively different in electrical conductivity and many other aspects. The available bulk-production methods generally yield mixtures of metallic and semiconducting SWNTs, despite continuing efforts in metallicity-selective nanotube growth. Presented here are significant advances and major achievements in the development of postproduction separation methods, which are now capable of harvesting separated metallic and semiconducting SWNTs from different production sources with sufficiently high enrichment and quantities for satisfying at least the needs in research and technological explorations. Opportunities and some available examples for the use of metallic SWNTs in transparent electrodes and semiconducting SWNTs in various device nanotechnologies are highlighted and discussed.
Prostatic androgen repressed message‐1 (PARM‐1) may play a role in prostatic cell immortalisation (2003)

Increased telomerase activity is often associated with the immortalisation of cancer cell lines, particularly prostatic ones. This could mean that PARM-1 is involved, via increased telomerase activity, in a survival program enabling certain prostatic cells to resist apoptosis, thus conferring a selective advantage to pre-cancerous or cancerous cells.
Efficient methods for high quality low bit rate wideband speech coding (2003)

This paper describes efficient encoding and decoding methods for achieving high quality wideband speech at low rates. CELP-based technologies have been successful in achieving high quality speech at low bit rates, however, new efficient techniques are needed to maintain high speech quality when the model is applied to wideband signals. This article discusses some techniques that improve the performance of the CELP model including efficient perceptual weighting and pitch codebook, and decoding techniques such as gain smoothing, periodicity enhancement, and high frequency generation. These techniques have been incorporated in the AMR-WB (adaptive multi-rate wideband) codec selected by 3GPP and ITU-T, where high quality wideband speech can be maintained at bit rates around 13 kbit/s.
Nitric oxide regulates matrix metalloproteinase-9 activity by guanylyl-cyclase-dependent and -independent pathways (2007)

Matrix metalloproteinases (MMPs) are of central importance in the proteolytic remodeling of matrix and the generation of biologically active molecules. MMPs are distinguished by a conserved catalytic domain containing a zinc ion, as well as a prodomain that regulates enzyme activation by modulation of a cysteine residue within that domain. Because nitric oxide (NO) and derived reactive nitrogen species target zinc ions and cysteine thiols, we assessed the ability of NO to regulate MMPs. A dose-dependent, biphasic regulatory effect of NO on the activity of MMPs (MMP-9, -1, and -13) secreted from murine macrophages was observed. Low exogenous NO perturbed MMP/tissue inhibitor of metalloproteinase (TIMP)-1 levels by enhancing MMP activity and suppressing the endogenous inhibitor TIMP-1. This was cGMP-dependent, as confirmed by the cGMP analog 8-bromo-cGMP, as well as by the NO-soluble guanylyl cyclase-cGMP signaling inhibitor thrombospondin-1. Exposure of purified latent MMP-9 to exogenous NO demonstrated a concentration-dependent activation and inactivation of the enzyme, which occurred at higher NO flux. These chemical reactions occurred at concentrations similar to that of activated macrophages. Importantly, these results suggest that NO regulation of MMP-9 secreted from macrophages may occur chemically by reactive nitrogen species-mediated protein modification, biologically through soluble guanylyl-cyclase-dependent modulation of the MMP-9/TIMP-1 balance, or proteolytically through regulation of MMP-1 and -13, which can cleave the prodomain of MMP-9. Furthermore, when applied in a wound model, conditioned media exhibiting peak MMP activity increased vascular cell migration that was MMP-9-dependent, suggesting that MMP-9 is a key physiologic mediator of the effects of NO in this model.
Receptor activator of nuclear ??B ligand and osteoprotegerin: where are we now and what about future treatment uses? (2005)

Purpose of review: Since the discovery of the RANK, its ligand, and osteoprotegerin as the final effectors of osteoclastogenesis and bone resorption, there has been an aggressive effort to develop a biologic antagonist of this pathway as a therapeutic for metabolic bone disease. While the early candidate osteoprotegerin molecules failed to meet clinical expectations, a human monoclonal antibody that recognizes RANKL (AMG162; Amgen, Inc., Thousand Oaks, California) is showing tremendous promise in phase II and phase III clinical trials. Here we review the trials and tribulations of RANK blockade for osteoporosis, tumor metastasis to bone, hypercalcemia of malignancy, inflammatory arthritis, and periprosthetic osteolysis. Recent findings: Although in-vitro studies have demonstrated RANKL-independent osteoclastogenesis and bone resorption, there is no evidence that this can occur in vivo. Furthermore, there are no preclinical models of metabolic bone disease that are refractory to RANK blockade. These studies have also demonstrated two critical advantages over bisphosphonate therapy. The first is that bone formation is not inhibited by RANK blockade such that anti-RANKL can be effectively used in combination with anabolic agents like parathyroid hormone, which is not true for alendronate. Second, RANK blockade is very effective in preventing erosions in the setting of inflammatory arthritis, and potentially aseptic loosening. Summary: Enrollment of the pivotal phase III clinical trial of AMG162 in women after menopause has been completed, and the results will be out in the next few years. If it is approved, the effective dosing regimen for patients will be subcutaneous injection of 60 mg every 6 months, which overcomes the gastrointestinal complications of oral bisphosphonates and should dramatically improve compliance. Moreover, anti-RANKL therapy may prove to be the long sought after intervention to prevent aseptic loosening in patients with established periprosthetic osteolysis.