gebhart/patrepeval huggingface dataset:
Study of the Binding of Iron and Indium to Human Serum Apo-Transferrin (2003)

Indium is a heavy metal belonging to group III a. It is believed that indium may interfere with iron metabolism from the sites of absorption, transportation, utilization an d storage in the cells. The present investigation was established to study and compare the binding of iron and indium to human apo-transferrin (apo-tf). Pure human apo-tf was used and the binding activity of iron and indium, as a complex with citric acid (1:20), to apo-tf was studied. The binding of iron and indium to apo -tf in TrisHCl buffer, pH 7.4 showed a maximum absorbance at 465 and 255 nm, respectively. The binding of both metals to apo-tf appears to be pH dependent. Using equilibrium dialysis tech nique, the binding of iron to apo-tf and the effect of indium on the binding process were also studied. Addition of indium to the outside of dialysis sac reduced iron uptake by 37%. The results indicate that indium competes with iron in binding to apo-tf. Although, the binding sites for these two ions seem to be similar, the binding of iron to apo-tf is more tightly than indium. Iran. Biomed. J. 7 (2): 73-77, 2003
Adaptive Sampling of Area Light Sources in Ray Tracing Including Diffuse Interreflection (1992)

Abstract Ray tracing algorithms that sample both the light received directly from light sources and the light received indirectly by diffuse reflection from other patches, can accurately render the global illumination in a scene and can display complex scenes with accurate shadowing. A drawback of these algorithms, however, is the high cost for sampling the direct light which is done by shadow ray testing. Although several strategies are available to reduce the number of shadow rays, still a large number of rays will be needed, in particular to sample large area light sources. An adaptive sampling strategy is proposed that reduces the number of shadow rays by using statistical information from the sampling process and by applying information from a radiosity preprocessing. A further reduction in shadow rays is obtained by applying shadow pattern coherence, i.e. reusing the adaptive sampling pattern for neighboring sampling points.
Combinatorial Approach to Flavor Analysis. 2. Olfactory Investigation of a Library of <i>S-</i>Methyl Thioesters and Sensory Evaluation of Selected Components (1999)

The odor characteristics of individual components present in a library comprised of S-methyl thioesters were determined independently by two laboratories using similar but not identical techniques. The odor potency was assessed by values of best estimate-GC-lower amount detected by sniffing (BE-GC-LOADS). For small and medium chain S-methyl thioesters, these values were found to increase from 6 ng for S-methyl thiobutanoate to 90 ng for S-methyl thiostearate. All assessors detected a "green", "floral", or "pineapple" odor for S-methyl thiohexanoate and described thioesters containing a 2-6 carbon chain length as "cheesy". The results of this preliminary analysis were confirmed by a more extensive study of selected compounds, namely S-methyl thioacetate, S-methyl thiopropionate, S-methyl thiobutanoate, and S-methyl thiohexanoate, using a trained panel of 18 subjects. The subjects confirmed the presence of the "green" and "fruity" notes in the odor of S-methyl thiohexanoate. The analysis also revealed a significant difference in the odor of S-methyl thiopropionate relative to that of S-methyl thioacetate and S-methyl thiobutanoate. When "cheesy" characteristics were mentioned, the majority of panelists clearly associated the flavor of S-methyl thiopropionate with Camembert with almost 20% of all the descriptors given referring specifically to this cheese variety as compared to about 2 and 5% in the case of S-methyl thioacetate and thiobutanoate, respectively. Prompted by this observation, two samples of Camembert prepared from unpasteurized and pasteurized milk were analyzed and relatively large amounts of S-methyl thiopropionate were found in the former but not in the latter cheese. The results obtained in the course of this work suggest that the sensory analysis of combinatorial libraries is a useful new approach in the search for new commercial flavors and/or identification of characteristic flavors in foods.
Protein surface analysis for function annotation in high‐throughput structural genomics pipeline (2005)

Structural genomics (SG) initiatives are expanding the universe of protein fold space by rapidly determining structures of proteins that were intentionally selected on the basis of low sequence similarity to proteins of known structure. Often these proteins have no associated biochemical or cellular functions. The SG success has resulted in an accelerated deposition of novel structures. In some cases the structural bioinformatics analysis applied to these novel structures has provided specific functional assignment. However, this approach has also uncovered limitations in the functional analysis of uncharacterized proteins using traditional sequence and backbone structure methodologies. A novel method, named pvSOAR (pocket and void Surface of Amino Acid Residues), of comparing the protein surfaces of geometrically defined pockets and voids was developed. pvSOAR was able to detect previously unrecognized and novel functional relationships between surface features of proteins. In this study, pvSOAR is applied to several structural genomics proteins. We examined the surfaces of YecM, BioH, and RpiB from Escherichia coli as well as the CBS domains from inosine-5'-monosphate dehydrogenase from Streptococcus pyogenes, conserved hypothetical protein Ta549 from Thermoplasm acidophilum, and CBS domain protein mt1622 from Methanobacterium thermoautotrophicum with the goal to infer information about their biochemical function.
Transcriptome Analysis of <i>Spermophilus lateralis</i> and <i>Spermophilus tridecemlineatus</i> Liver Does Not Suggest the Presence of Spermophilus-Liver-Specific Reference Genes (2013)

The expressions of reference genes used in gene expression studies are assumed to be stable under most circumstances. However, studies had demonstrated that genes assumed to be stably expressed in a species are not necessarily stably expressed in other organisms. This study aims to evaluate the likelihood of genus-specific reference genes for liver using comparable microarray datasets from Spermophilus lateralis and Spermophilus tridecemlineatus. The coefficient of variance (CV) of each probe was calculated and there were 178 probes common between the lowest 10% CV of both datasets (n = 1258). All 3 lists were analysed by NormFinder. Our results suggest that the most invariant probe for S. tridecemlineatus was 02n12, while that for S. lateralis was 24j21. However, our results showed that Probes 02n12 and 24j21 are ranked 8644 and 926 in terms of invariancy for S. lateralis and S. tridecemlineatus respectively. This suggests the lack of common liver-specific reference probes for both S. lateralis and S. tridecemlineatus. Given that S. lateralis and S. tridecemlineatus are closely related species and the datasets are comparable, our results do not support the presence of genus-specific reference genes.
Improved half RF slice selectivity in the presence of eddy currents with out‐of‐slice saturation (2009)

Ultrashort echo time imaging with half RF pulse excitation is sensitive to eddy currents induced by the slice-select gradient that distorts the half pulse slice profile. This work demonstrates improvements in the half pulse profile by using spatial saturation on both sides of the imaged slice to suppress the out-of-slice magnetization. This effectively improves the selectivity of the half pulse excitation profile. A quadratic phase RF pulse with high bandwidth and selectivity was used to achieve a wide saturation band with sharp edges. Experimental results demonstrate substantially improved slice selectivity and R(2)* quantitation accuracy obtained with the out-of-slice saturation. This approach is effective in making short T(2) imaging and quantitation with half pulses less sensitive to eddy currents.
Lubrication forces between surfaces bearing polymer brushes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLubrication forces between surfaces bearing polymer brushesJacob Klein, Yoichiro Kamiyama, Hisae Yoshizawa, Jacob N. Israelachvili, Glenn H. Fredrickson, Philip Pincus, and Lewis J. FettersCite this: Macromolecules 1993, 26, 21, 5552–5560Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ma00073a004https://doi.org/10.1021/ma00073a004research-articleACS PublicationsRequest reuse permissionsArticle Views1167Altmetric-Citations207LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Conventional and quantitative EEG in the diagnosis of delirium among the elderly. (1993)

This study was performed to determine whether an admission quantitative EEG (QEEG) could assist in the differential diagnosis of encephalopathy among a group of elderly subjects with delirium, dementia, and delirium coexistent with dementia. Thirty four subjects from 57 to 93 years had standard 17-channel EEG and quantitative EEG studies, using a linked-ear reference. EEGs were independently rated by two electroencephalographers blind to clinical diagnosis, using conventional criteria to assess the degree of encephalopathy. Brain maps were scored by a scale developed by the authors. Numerical data examined included mean posterior dominant frequency, absolute and relative power in the delta, theta and alpha bands, and slow-wave ratios. The grouping of experimental subjects was by the discharge diagnosis, made using DSM-III-R criteria. Stepwise discriminant analysis was performed to determine which EEG and QEEG variables were best able to distinguish cases. Variables which collectively distinguished normal from encephalopathic records were Mini-Mental State Examination scores and relative power in the alpha frequency band. Variables which collectively distinguished delirium from dementia were EEG theta activity, relative power in delta, and brain map rating. The results suggest that cross-sectional QEEG study is potentially useful in the early differential diagnosis of encephalopathy, and that the variables which distinguish normal from encephalopathic patients might differ from the variables which distinguish delirium from dementia.
Real-time MRI guided percutaneous transthoracic left ventricular access and closure (2011)

Introduction and objective Percutaneous transthoracic left ventricular (LV) access and closure would be an enabling technology for a wide range of structural heart, electrophysiologic and proximal aorta procedures. We propose a real-time MRI guided approach to access and close the LV using novel active devices. Methods Sixteen Yorkshire swine underwent percutaneous transthoracic LV access and followed up to three months (n=8). All procedures were guided by real-time bSSFP MRI (Espree, Siemens) using two slices along the needle trajectory and a short-axis slice for cardiac monitoring. Transthoracic ventricular puncture was performed using a customized 18G active needle with integrated loop coil. Puncture trajectory was planned using realtime MRI to identify optimal LV puncture target and trajectory with respect to intraventricular and valvular structures (Figure 1A). After needle entry, an 18-French sheath was inserted and anticoagulation begun.
[Clinical heterogeneity of the autistic syndrome: a study of 60 families]. (1992)

Sixty families ascertained through a single proband, has helped to better define infantile autism as a heterogeneous group of disorders. Forty four patients showed a characteristic facio- auricular dysplasia. Twenty four of these, showed increased pyruvate and lactate and laboratory findings of metabolic acidosis i.e., anion gap above 18 mEq/L or serum bicarbonate below 21 mEq/L but only nine of these probands demonstrated reduction of plasma bicarbonate below 18 mEq/lt. Plasma amino acids in 17 probands and matched controls showed increased taurine with the rest of amino acids significantly (p less than 0.05) below the control level. Glutamate and aspartate were also significantly elevated (p less than 0.05; Student t-test). Segregation analysis in thirty four of these families which linked through at least one ancestral family name, suggested autosomal recessive inheritance (p = 0.20). Three out of eight probands who received megadoses of pyridoxine (Vitamin B6), subjectively gained in language abilities, affectivity and response to behavior modification therapy. Five autistic patients proved to have clinically defined syndromes: two with the Martin-Bell syndrome, and three girls affected respectively with the Rett syndrome, phenylketonuria and dicarboxylic aciduria.
Cunninghamella Infections: Review and Report of Two Cases of Cunninghamella Pneumonia in Immunocompromised Children (1993)

Infections caused by Cunninghamella bertholletiae are being identified with increasing frequency in immunocompromised patients. We have treated two children with cancer for pulmonary infections caused by this rare fungus. Cunninghamella infection is found in a variety of populations of patients, including both children and adults undergoing chemotherapy. Clinical signs and symptoms are indistinguishable from those of other forms of zygomycosis. Outcome is poor: only three of 17 patients with such infection (including one of the two children described herein) have survived. Treatment involves aggressive surgical excision and administration of amphotericin B.
Total Synthesis and Biological Evaluation of Tamandarin B Analogues (2007)

Tamandarins A and B are a class of marine natural cyclodepsipeptides with structures and biological activities closely related to those of the didemnins. The easier synthetic access to tamandarins accelerates the preparation of new macrocyclic derivatives of this family of antitumor, antiviral, and immunosuppressive compounds. The optimization of the previously reported synthetic route to tamandarins by changing the macrolactamization site from Nst1 and Thr6 to Pro4 and N,O-Me2Tyr5 residues led to a significant improvement in the reaction yield. Using this new synthetic approach, four new macrocyclic analogues of tamandarin B were prepared and evaluated for anticancer activity. These results provide further insight into the structure-activity relationship of the tamandarins and didemnins.
Mlps (mono layer polynomials and multi layer perceptrons) for nonlinear modeling (2003)

This paper presents a model selection procedure which stresses the importance of the classic polynomial models as tools for evaluating the complexity of a given modeling problem, and for removing non-significant input variables. If the complexity of the problem makes a neural network necessary, the selection among neural candidates can be performed in two phases. In an additive phase, the most important one, candidate neural networks with an increasing number of hidden neurons are trained. The addition of hidden neurons is stopped when the effect of the round-off errors becomes significant, so that, for instance, confidence intervals cannot be accurately estimated. This phase leads to a set of approved candidate networks. In a subsequent subtractive phase, a selection among approved networks is performed using statistical Fisher tests. The series of tests starts from a possibly too large unbiased network (the full network), and ends with the smallest unbiased network whose input variables and hidden neurons all have a significant contribution to the regression estimate. This method was successfully tested against the real-world regression problems proposed at the NIPS2000 Unlabeled Data Supervised Learning Competition; two of them are included here as illustrative examples.
iPIM: Programmable In-Memory Image Processing Accelerator Using Near-Bank Architecture (2020)

Image processing is becoming an increasingly important domain for many applications on workstations and the datacenter that require accelerators for high performance and energy efficiency. GPU, which is the state-of-the-art accelerator for image processing, suffers from the memory bandwidth bottleneck. To tackle this bottleneck, near-bank architecture provides a promising solution due to its enormous bank-internal bandwidth and low-energy memory access. However, previous work lacks hardware programmability, while image processing workloads contain numerous heterogeneous pipeline stages with diverse computation and memory access patterns. Enabling programmable near-bank architecture with low hardware overhead remains challenging.This work proposes iPIM, the first programmable in-memory image processing accelerator using near-bank architecture. We first design a decoupled control-execution architecture to provide lightweight programmability support. Second, we propose the SIMB (Single-Instruction-Multiple-Bank) ISA to enable flexible control flow and data access. Third, we present an end-to-end compilation flow based on Halide that supports a wide range of image processing applications and maps them to our SIMB ISA. We further develop iPIM-aware compiler optimizations, including register allocation, instruction reordering, and memory order enforcement to improve performance. We evaluate a set of representative image processing applications on iPIM and demonstrate that on average iPIM obtains 11.02× acceleration and 79.49% energy saving over an NVIDIA Tesla V100 GPU. Further analysis shows that our compiler optimizations contribute 3.19× speedup over the unoptimized baseline.
Semantic Modeling for Cloud Computing, Part 1 (2010)

Cloud computing has lately become the attention grabber in both academia and industry. The promise of seemingly unlimited, readily available utility-type computing has opened many doors previously considered difficult, if not impossible, to open. The cloud computing landscape, however, is still evolving, and we must overcome many challenges to foster widespread adoption of clouds. The main challenge is interoperability.
Automated generation of libraries of nL droplets (2012)

We demonstrate an integrated system for rapid and automated generation of multiple, chemically distinct populations of ~10(3)-10(4) sub-nanoliter droplets. Generation of these 'libraries of droplets' proceeds in the following automated steps: i) generation of a sequence of micro-liter droplets of individually predetermined composition, ii) injection of these 'parental' droplets onto a chip, iii) transition from a mm- to a μm-scale of the channels and splitting each of the parental drops with a flow-focusing module into thousands of tightly monodisperse daughter drops and iv) separation of such formed homogeneous populations with plugs of a third immiscible fluid. This method is compatible both with aspiration of microliter portions of liquid from a 96-well plate with a robotic station and with automated microfluidic systems that generate (~μL) droplets of preprogrammed compositions. The system that we present bridges the techniques that provide elasticity of protocols executed on microliter droplets with the techniques for high-throughput screening of small (~pL, ~nL) droplet libraries. The method that we describe can be useful in exploiting the synergy between the ability to rapidly screen distinct chemical environments and to perform high-throughput studies of single cells or molecules and in digital droplet PCR systems.
Mistletoe extract standardized for the galactoside-specific lectin (ML-1) induces beta-endorphin release and immunopotentiation in breast cancer patients. (1994)

The ability of immunomodulating mistletoe extract standardized for the galactoside-specific lectin (ML-1) to affect immunological parameters (peripheral blood lymphocyte counts, cytokine release) as well as neuroendocrinological parameters (beta-endorphin release) was investigated in breast cancer patients (n = 36). Regular subcutaneous injections of the optimal immunomodulating ML-1 dosage (1ng/kg body weight, twice a week) for 12 weeks induced 1) a significant increase (p < 0.005) of beta-endorphin plasma levels, 2) a reduced decrease (respectively moderate increase) of defined peripheral blood lymphatic subsets after standard chemotherapy, 3) an evidently increased in vitro cytokine release by mononuclear immune cells after adequate stimulation. The increased levels of plasma beta-endorphin after ML-1 administration obviously correlate with an improved quality of life in this group of patients; however, increased in vitro cytokine release and stabilization of peripheral blood lymphocyte counts after chemotherapy demonstrate the immunoactive potency of ML-1.
Diversity of Borrelia burgdorfeii Sensu Lato Evidenced by Restriction Fragment Length Polymorphism of rrf (5S)-rrl (23S) Intergenic Spacer Amplicons (1994)

The organization of the ribosomal genes is unique in Borrelia burgdorferi in that the rrl (23S) and rrf (5S) genes are tandemly duplicated. We took advantage of this uniqueness to assess the restriction polymorphism of PCR products obtained with primers at the 3' end of the first rrf gene and at the 5' end of the second rrl gene. An amplicon that was 226 to 266 bp long was generated from 99 to 100 B. burgdorferi sensu lato strains. The nuclease MseI restriction polymorphism of the amplicons provided a useful tool for identifying B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii (formerly group VS461), and Borrelia japonica (formerly group F63B). Furthermore, it allowed us to recognize four new genomic groups, which were confirmed by DNA-DNA hybridization data. Two of these genomic groups comprised European strains, and the other two groups contained American strains. The American genomic groups involved vectors with enzootic cycles quite different from those of B. burgdorferi sensu stricto, which previously was the only Lyme disease Borrelia species known to occur in the United States. Our method could be used for rapid screening of strain collections and for epidemiological and medical purposes.