gebhart/patrepeval huggingface dataset:
In vitro formation of "urinary stones": generation of spherulites of calcium phosphate in gel and overgrowth with calcium oxalate using a new flow model of crystallization. (1995)

Calcium phosphate (CaP) has been detected in the majority of urinary stones containing predominantly calcium oxalate (CaOx). Therefore, crystal phases of CaP might play an important role with respect to the formation of urinary calcium stones in general. Very often, CaP found in stones or tissue of human kidney occurs in the shape of small spherulites. In this paper, we report on a new flow model of crystallization (FMCG), which has been used to generate spherulites of CaP in a gel matrix of 1% agar-agar at 37 degrees C from a supersaturated, metastable solution continuously flowing over the gel surface. Scanning electron microscopy (SEM), X-ray diffraction and microscopic Fourier transformed infrared spectroscopy (FTIR) revealed that the particles formed (diameter: up to 200 microns) consisted of a poorly crystalline core of carbonatoapatite which was partly surrounded by a well-crystallized shell of octacalcium phosphate (OCP) showing radially oriented sheet-like structures. Subsequently, CaOx was grown on these spherulites from a flow of a correspondingly supersaturated solution conducted over the gel matrix. It could be shown by SEM that growth of calcium oxalate monohydrate (COM) was characteristically induced by the OCP shell. Radial sheet-like forms of OCP were directly continued by COM showing a certain radial orientation. The model of crystallization in gel matrices applied here should be well-suited to simulate the process of urinary stone formation under in vitro conditions.
Experiences with making diffraction image data available: what metadata do we need to archive? (2014)

Recently, the IUCr (International Union of Crystallography) initiated the formation of a Diffraction Data Deposition Working Group with the aim of developing standards for the representation of raw diffraction data associated with the publication of structural papers. Archiving of raw data serves several goals: to improve the record of science, to verify the reproducibility and to allow detailed checks of scientific data, safeguarding against fraud and to allow reanalysis with future improved techniques. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. In a recent study of the binding of cisplatin and carboplatin to histidine in lysozyme crystals under several conditions, the possible effects of the equipment and X-ray diffraction data-processing software on the occupancies and B factors of the bound Pt compounds were compared. Initially, 35.3 GB of data were transferred from Manchester to Utrecht to be processed with EVAL. A detailed description and discussion of the availability of metadata was published in a paper that was linked to a local raw data archive at Utrecht University and also mirrored at the TARDIS raw diffraction data archive in Australia. By making these raw diffraction data sets available with the article, it is possible for the diffraction community to make their own evaluation. This led to one of the authors of XDS (K. Diederichs) to re-integrate the data from crystals that supposedly solely contained bound carboplatin, resulting in the analysis of partially occupied chlorine anomalous electron densities near the Pt-binding sites and the use of several criteria to more carefully assess the diffraction resolution limit. General arguments for archiving raw data, the possibilities of doing so and the requirement of resources are discussed. The problems associated with a partially unknown experimental setup, which preferably should be available as metadata, is discussed. Current thoughts on data compression are summarized, which could be a solution especially for pixel-device data sets with fine slicing that may otherwise present an unmanageable amount of data.
RETRACTED: Downregulation of miR‐122 in the rodent and human hepatocellular carcinomas (2006)

MicroRNAs (miRs) are conserved small non-coding RNAs that negatively regulate gene expression. The miR profiles are markedly altered in cancers and some of them have a causal role in tumorigenesis. Here, we report changes in miR expression profile in hepatocellular carcinomas (HCCs) developed in male Fisher rats-fed folic acid, methionine, and choline-deficient (FMD) diet. Comparison of the miR profile by microarray analysis showed altered expression of some miRs in hepatomas compared to the livers from age-matched rats on the normal diet. While let-7a, miR-21, miR-23, miR-130, miR-190, and miR-17-92 family of genes was upregulated, miR-122, an abundant liver-specific miR, was downregulated in the tumors. The decrease in hepatic miR-122 was a tumor-specific event because it did not occur in the rats switched to the folate and methyl-adequate diet after 36 weeks on deficient diet, which did not lead to hepatocarcinogenesis. miR-122 was also silent in a transplanted rat hepatoma. Extrapolation of this study to human primary HCCs revealed that miR-122 expression was significantly (P = 0.013) reduced in 10 out of 20 tumors compared to the pair-matched control tissues. These findings suggest that the downregulation of miR-122 is associated with hepatocarcinogenesis and could be a potential biomarker for liver cancers.
The cortical serotonin2Areceptor and the pathology of schizophrenia: a likely accomplice (2003)

A large body of evidence shows that there is a change in the density of cortical serotonin2A receptors (5HT2AR) in post-mortem CNS from subjects with schizophrenia. Furthermore, some antipsychotic drugs have also been shown to cause a decrease in the density of 5HT2AR in the rat CNS. Thus, it appeared possible that changes in this receptor in human post-mortem CNS simply reflected an antipsychotic drug effect. However, a great deal of research on the 5HT2AR and schizophrenia now suggests that the changes in this receptor are complex and may be involved in both the pathology of the disorder and the effects of some antipsychotic drugs. Moreover, recent advances in basic research on the role of the 5HT2AR in the CNS add further support to the hypothesis that the receptor could be involved in the pathology of the illness. In particular, an argument will be developed that the changes in the 5HT2AR in schizophrenia are reflective of a real or perceived change in serotonergic tone and that this forms an important part of the pathology of the illness.
Purification and Amino Acid Sequence of Kunitz-Type Protease Inhibitor Found in the Hemocytes of Horseshoe Crab (Tachypleus tridentatus)12 (1987)

A low molecular weight protein protease inhibitor was purified from Japanese horseshoe crab (Tachypleus tridentatus) hemocytes. It consisted of a single polypeptide with a total of 61 amino acid residues. This protease inhibitor inhibited stoichiometrically the amidase activity of trypsin (Ki = 4.60 X 10(-10) M), and also had inhibitory effects on alpha-chymotrypsin (Ki = 5.54 X 10(-9) M), elastase (Ki = 7.20 X 10(-8) M), plasmin, and plasma kallikrein. However, it had no effect on T. tridentatus clotting enzyme and factor C, mammalian blood coagulation factors (activated protein C, factor Xa and alpha-thrombin), papain, and thermolysin. The complete amino acid sequence of this inhibitor was determined and its sequence was compared with those of bovine pancreatic trypsin inhibitor (BPTI) and other Kunitz-type inhibitors. It was found that the amino acid sequence of this inhibitor has a high homology of 47 and 43% with those of sea anemone inhibitor 5-II and BPTI, respectively. Thus, this protease inhibitor appeared to be one of the typical Kunitz-type protease inhibitors.
A New Academic Word List (2000)

This article describes the development and evaluation of a new academic word list (Coxhead, 1998), which was compiled from a corpus of 3.5 million running words of written academic text by examining the range and frequency of words outside the first 2,000 most frequently occurring words of English, as described by West (1953). The AWL contains 570 word families that account for approximately 10.0% of the total words (tokens) in academic texts but only 1.4% of the total words in a fiction collection of the same size. This difference in coverage provides evidence that the list contains predominantly academic words. By highlighting the words that university students meet in a wide range of academic texts, the AWL shows learners with academic goals which words are most worth studying. The list also provides a useful basis for further research into the nature of academic vocabulary.
Norm estimates of interpolation matrices and their inverses associated with strictly positive definite functions (1999)

In this paper, we estimate the norms of the interpolation matrices and their inverses that arise from scattered data interpolation on spheres with strictly positive definite functions.
The Ligands for Human IgG and Their Effector Functions (2019)

Activation of the humoral immune system is initiated when antibodies recognize an antigen and trigger effector functions through the interaction with Fc engaging molecules. The most abundant immunoglobulin isotype in serum is Immunoglobulin G (IgG), which is involved in many humoral immune responses, strongly interacting with effector molecules. The IgG subclass, allotype, and glycosylation pattern, among other factors, determine the interaction strength of the IgG-Fc domain with these Fc engaging molecules, and thereby the potential strength of their effector potential. The molecules responsible for the effector phase include the classical IgG-Fc receptors (FcγR), the neonatal Fc-receptor (FcRn), the Tripartite motif-containing protein 21 (TRIM21), the first component of the classical complement cascade (C1), and possibly, the Fc-receptor-like receptors (FcRL4/5). Here we provide an overview of the interactions of IgG with effector molecules and discuss how natural variation on the antibody and effector molecule side shapes the biological activities of antibodies. The increasing knowledge on the Fc-mediated effector functions of antibodies drives the development of better therapeutic antibodies for cancer immunotherapy or treatment of autoimmune diseases.
Rapid acquisition algorithms for synchronization of bursty transmissions in CDMA microcellular and personal wireless systems (1996)

Two rapid synchronization acquisition algorithms applicable to spread spectrum links of code division multiple access (CDMA) personal communication systems are proposed and evaluated. The algorithms operate within a self-referencing matched filter synchronizer structure, and are particularly useful in reducing synchronization overhead on links designed to carry packet-type services. The main distinguishing characteristic between the two schemes is that one uses hard-decision while the other uses soft-decision detection. The proposed schemes are especially applicable to reverse link transmissions in quasisynchronous CDMA systems in which timing at portable terminals is established via pilot and synchronization signals received on respective code-division channels from the home base. If discontinuous (bursty) transmission is used on reverse links, the acquisition process is required for each transmission burst because of the propagation time uncertainty. Analysis of the algorithms on additive white Gaussian noise (AWGN) and Rayleigh fading channels reveals that their performance depends significantly on the choice of synchronizer parameters and the average despread signal-to-interference ratio (SIR). When this choice is proper, acquisition over a single preamble of relatively short duration can be achieved with high probability. The soft-decision scheme introduces a performance advantage of between 4-9 dB depending on the length of the synchronizing preamble.
May 2006 update in porphobilinogen deaminase gene polymorphisms and mutations causing acute intermittent porphyria. Comparison with the situation in Slavic population (2006)

Acute intermittent porphyria (AIP) is an autosomal dominant disorder of heme biosynthesis caused by molecular defects in the porphobilinogen deaminase (PBGD) gene. This paper reviews published mutations, their types, and polymorphisms within the PBGD gene. To date, 301 different mutations and 21 polymorphisms have been identified in the PBGD gene in AIP patients and individuals from various countries and ethnic groups. During the search for mutations identified among Slavic AIP patients we found 65 such mutations and concluded that there is not a distinct predominance of certain mutations in Slavs.
ICB database: the gyrB database for identification and classification of bacteria (2001)

The Identification and Classification of Bacteria (ICB) database (http:/www.mbio.co.jp/icb) contains currently available information about the DNA gyrase subunit B (gyrB) gene in bacteria. The database is designed to provide the scientific community with a reference point for using gyrB as an evolutionary and taxonomic marker. Nucleic and amino acid sequence data are currently available for over 850 strains, along with alignments at several different taxonomic levels and an exhaustive review of primer selection and background information.
The weighted periodic function and its properties (2006)

In addition to the concept of tile normal periodic function and the almost periodic function, a new concept of the weighted periodic function is proposed. Due to the particularity of this kind of functions, the properties are also investigated.
Allelotype of pancreatic adenocarcinoma using xenograft enrichment. (1995)

p53 and MTS1 are known to be mutationally inactivated in pancreatic adenocarcinoma. Other tumor suppressor genes are likely also to play a role. To define chromosomal arms which may harbor additional tumor suppressor genes, we performed an extensive allelotype on pancreatic cancer utilizing a xenograft enrichment technique. Eighty-eight percent (28/32) of primary tumors gave rise to xenografts. Eighteen cases were used in a PCR-based allelotype using 283 polymorphic markers, over 2800 informative assays, and an average coverage of 4.1 informative markers per chromosomal arm per case. Highly frequent allelic loss (> 60%) was seen at chromosomes 1p, 9p, 17p, and 18q. Moderately frequent allelic loss (40-60%) was seen at 3p, 6p, 6q, 8p, 10q, 12q, 13q, 18p, 21q, and 22q. The average fractional allelic loss was 0.36. Allelic and sequence stability was demonstrated among 64 parallel and second-passage xenografts derived from 12 cases of pancreatic adenocarcinoma with the ascertainment of over 3000 single alleles. The findings were confirmed in primary tumors. In only two instances were discrepancies revealed between the allelic loss data obtained from corresponding parallel xenografts, probably due to the xenografting of minor subpopulations, reflecting genetic heterogeneity of the primary tumor.
Error Correcting Codes in Quantum Theory (1996)

A new type of uncertainty relation is presented, concerning the information-bearing properties of a discrete quantum system. A natural link is then revealed between basic quantum theory and the linear error correcting codes of classical information theory. A subset of the known codes is described, having properties which are important for error correction in quantum communication. It is shown that a pair of states which are, in a certain sense, "macroscopically different," can form a superposition in which the interference phase between the two parts is measurable. This provides a highly stabilized "Schrödinger cat" state.Received 4 October 1995DOI:https://doi.org/10.1103/PhysRevLett.77.793©1996 American Physical Society
Cardiotrophin-1, a Muscle-Derived Cytokine, Is Required for the Survival of Subpopulations of Developing Motoneurons (2001)

Developing motoneurons require trophic support from their target, the skeletal muscle. Despite a large number of neurotrophic molecules with survival-promoting activity for isolated embryonic motoneurons, those factors that are required for motoneuron survival during development are still not known. Cytokines of the ciliary neurotrophic factor (CNTF)-leukemia inhibitory factor (LIF) family have been shown to play a role in motoneuron (MN) survival. Importantly, in mice lacking the LIFRbeta or the CNTFRalpha there is a significant loss of MNs during embryonic development. Because genetic deletion of either (or both) CNTF or LIF fails, by contrast, to perturb MN survival before birth, it was concluded that another ligand exists that is functionally inactivated in the receptor deleted mice, resulting in MN loss during development. One possible candidate for this ligand is the CNTF-LIF family member cardiotrophin-1 (CT-1). CT-1 is highly expressed in embryonic skeletal muscle, secreted by myotubes, and promotes the survival of cultured embryonic mouse and rat MNs. Here we show that ct-1 deficiency causes increased motoneuron cell death in spinal cord and brainstem nuclei of mice during a period between embryonic day 14 and the first postnatal week. Interestingly, no further loss was detectable during the subsequent postnatal period, and nerve lesion in young adult ct-1-deficient mice did not result in significant additional loss of motoneurons, as had been previously observed in mice lacking both CNTF and LIF. CT-1 is the first bona fide muscle-derived neurotrophic factor to be identified that is required for the survival of subgroups of developing motoneurons.
Nonlinear X-Wave Ultrasound Imaging of Acoustic Biomolecules (2018)

The basic physics of sound waves enables ultrasound to visualize biological tissues with high spatial and temporal resolution. Recently, this capability was enhanced with the development of acoustic biomolecules - proteins with physical properties enabling them to scatter sound. The expression of these unique air-filled proteins, known as gas vesicles (GVs), in cells allows ultrasound to image cellular functions such as gene expression <i>in vivo</i>, providing ultrasound with its analog of optical fluorescent proteins. Acoustical methods for the <i>in vivo</i> detection of GVs are now required to maximize the impact of this technology in biology and medicine. We previously engineered GVs exhibiting a nonlinear scattering behavior in response to acoustic pressures above 300 kPa, and showed that amplitude-modulated (AM) ultrasound pulse sequences that both excite the linear and nonlinear GV scattering regimes were highly effective at distinguishing GVs from linear scatterers like soft biological tissues. Unfortunately, the <i>in vivo</i> specificity of AM ultrasound imaging is systematically compromised by the nonlinearity added by the GVs to propagating waves, resulting in strong image artifacts from linear scatterers downstream of GV inclusions. To address this issue, we present an imaging paradigm, cross-amplitude modulation (xAM), which relies on cross-propagating plane-wave transmissions of finite aperture X-waves to achieve quasi artifact-free <i>in vivo</i> imaging of GVs. The xAM method derives from counter-propagating wave interaction theory which predicts that, in media exhibiting quadratic elastic nonlinearity like biological tissue, the nonlinear interaction of counter-propagating acoustic waves is inefficient. By transmitting cross-propagating plane-waves, we minimize cumulative nonlinear interaction effects due to collinear wave propagation, while generating a transient wave-amplitude modulation at the two plane-waves' intersection. We show in both simulations and experiments that residual xAM nonlinearity due to wave propagation decreases as the plane-wave cross-propagation angle increases. We demonstrate in tissue-mimicking phantoms that imaging artifacts distal to GV inclusions decrease as the plane-wave cross-propagation angle opens, nearing complete extinction at angles above 16.5 degrees. Finally, we demonstrate that xAM enables highly specific <i>in vivo</i> imaging of GVs located in the gastrointestinal tract, a target of prime interest for future cellular imaging. These results advance the physical facet of the emerging field of biomolecular ultrasound, and are also relevant to synthetic ultrasound contrast agents.
Amyloid-Beta Immunotherapy for the Prevention and Treatment of Alzheimer Disease: Lessons from Mice, Monkeys, and Humans (2006)

Alzheimer disease (AD), the most common form of dementia, is without an effective cure or preventive treatment. Recently, amyloid-beta protein (Abeta) has become a major therapeutic target. Many efforts are underway to either reduce the production of Abeta or enhance its clearance. In 1999, Schenk and colleagues first showed that active immunization with full-length Abeta lowered cerebral Abeta levels in transgenic mice. These findings have been confirmed and extended in various transgenic mouse models of AD using both active and passive Abeta immunization. Cognitive improvement also has been reported in association with active and passive Abeta vaccination in AD-like mouse models, even in the absence of significant reductions in cerebral Abeta loads. In 2004, the authors reported that active immunization with full-length Abeta in aged nonhuman primates, Caribbean vervets, reduced cerebral Abeta levels and gliosis. Proposed mechanisms of Abeta clearance by immunotherapy include disruption of Abeta aggregates, Abeta phagocytosis by microglia, neutralization of Abeta oligomers at the synapse, and increased efflux of Abeta from brain to blood. A phase IIa clinical trial was halted in 2002 because of the appearance of meningoencephalitis in approximately 6% of the AD patients. Although the exact cause of these adverse events is unknown, the immunogen, full-length Abeta1-42, may have been recognized as a self-antigen leading to an autoimmune response in some patients. Limited cognitive stabilization and apparent plaque clearance have been reported in subsets of patients who generated antibody titers. Currently, a passive immunization trial with a recombinant humanized monoclonal Abeta antibody is underway in humans. In the meantime, the authors are developing novel Abeta peptide immunogens for active immunization to target Abeta B cell epitope(s) and avoid Abeta-specific T-cell reactions in order to generate a safe and effective AD vaccine. The authors remain optimistic about the potential of such a vaccine for the prevention and treatment of AD.
Molecular Biology of Bone Metastasis (2007)

Metastasis is a final stage of tumor progression. Breast and prostate cancer cells preferentially metastasize to bone, wherein they cause incurable osteolytic and osteoblastic lesions. The bone matrix is rich in factors, such as transforming growth factor-beta and insulin-like growth factors, which are released into the tumor microenvironment by osteolysis. These factors stimulate the growth of tumor cells and alter their phenotype, thus promoting a vicious cycle of metastasis and bone pathology. Physical factors within the bone microenvironment, including low oxygen levels, acidic pH, and high extracellular calcium concentrations, may also enhance tumor growth. These elements of the microenvironment are potential targets for chemotherapeutic intervention to halt tumor growth and suppress bone metastasis.