gebhart/patrepeval huggingface dataset:
Neu3 neuraminidase induction triggers intestinal inflammation and colitis in a model of recurrent human food-poisoning (2021)

Intestinal inflammation is the underlying basis of colitis and the inflammatory bowel diseases. These syndromes originate from genetic and environmental factors that remain to be fully identified. Infections are possible disease triggers, including recurrent human food-poisoning by the common foodborne pathogen <i>Salmonella enterica</i> Typhimurium (<i>ST</i>), which in laboratory mice causes progressive intestinal inflammation leading to an enduring colitis. In this colitis model, disease onset has been linked to Toll-like receptor-4-dependent induction of intestinal neuraminidase activity, leading to the desialylation, reduced half-life, and acquired deficiency of anti-inflammatory intestinal alkaline phosphatase (IAP). Neuraminidase (Neu) inhibition protected against disease onset; however, the source and identity of the Neu enzyme(s) responsible remained unknown. Herein, we report that the mammalian Neu3 neuraminidase is responsible for intestinal IAP desialylation and deficiency. Absence of Neu3 thereby prevented the accumulation of lipopolysaccharide-phosphate and inflammatory cytokine expression in providing protection against the development of severe colitis.
SARS-CoV-2 Spike Structure Vector Analysis Scripts and Molecular dynamics simulation trajectories for the SARS-CoV-2 WT and Mut (K417N+E484K+N501Y) RBDs (2021)

This entry contains filtered trajectories for both the WT and Mut (K417N+E484K+N501Y) datasets and the scripts used for the vector relationship and Markov modelling work in our paper "Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity" posted on bioRxiv March 12th 2021. The VMD scripts can be run from the tcl console after loading VMD and your structure or via the command line using: vmd -dispdev none -e script_name.tcl your_SARS-CoV-2_structure.pdb Residue numbers in these scripts are specific to SARS-CoV-2 and must be numbered in a manner consistent with the the PDB ID 6VXX structure. Analysis of other Coronavirus Spike structures will require modification of the residue selections. Tcl commands for visulizing the vectors in VMD are provided at the bottom of each VMD script. The HTMD.py script commands can be run in an interactive python session to allow for modification of the model and/or testing alternative projections, etc. This requires installation of HTMD (https://software.acellera.com/install-htmd.html). Filtered trajectories for both the WT and Mut (K417N+E484K+N501Y) datasets are available through Globus (https://www.globus.org/) via the following link: https://app.globus.org/file-manager?origin_id=aa7c9c4c-8343-11eb-b799-f57b2d55370d&amp;origin_path=%2F
Data Processing (1995)

The “digital revolution” changed seismic exploration beginning in the early 1960s, about 20 years before the widespread use of CDs in recorded music. The changes were of the same kind: much less noise, no deterioration of signal by repeated processing (playing), and the ability to reshape the information content into more easily understood forms.
Using inverse Laplace transform in positronium lifetime imaging (2022)

Positronium (Ps) lifetime imaging is gaining attention to bring out additional biomedical information from positron emission tomography (PET). The lifetime of Ps<i>in vivo</i>can change depending on the physical and chemical environments related to some diseases. Due to the limited sensitivity, Ps lifetime imaging may require merging some voxels for statistical accuracy. This paper presents a method for separating the lifetime components in the voxel to avoid information loss due to averaging. The mathematics for this separation is the inverse Laplace transform (ILT), and the authors examined an iterative numerical ILT algorithm using Tikhonov regularization, namely CONTIN, to discriminate a small lifetime difference due to oxygen saturation. The separability makes it possible to merge voxels without missing critical information on whether they contain abnormally long or short lifetime components. The authors conclude that ILT can compensate for the weaknesses of Ps lifetime imaging and extract the maximum amount of information.
Interfacial glass transition profiles in ultrathin, spin cast polymer films (2004)

Interfacial glass transition temperature (T(g)) profiles in spin cast, ultrathin films of polystyrene and derivatives were investigated using shear-modulated scanning force microscopy. The transitions were measured as a function of film thickness (delta), molecular weight, and crosslinking density. The T(g)(delta) profiles were nonmonotonic and exhibited two regimes: (a) a sublayer extending about 10 nm from the substrate, with T(g) values lowered up to approximately 10 degrees C below the bulk value, and (b) an intermediate regime extending over 200 nm beyond the sublayer, with T(g) values exceeding the bulk value by up to 10 degrees C. Increasing the molecular weight was found to shift the T(g)(delta) profiles further from the substrate interface, on the order of 10 nm/kDa. Crosslinking the precast films elevated the absolute T(g) values, but had no effect on the spatial length scale of the T(g)(delta) profiles. These results are explained in the context of film preparation history and its influence on molecular mobility. Specifically, the observed rheological anisotropy is interpreted based on the combined effects of shear-induced structuring and thermally activated interdiffusion.
Bioinformatics Strategies for Translating Genome‐Wide Expression Analyses into Clinically Useful Cancer Markers (2004)

The DNA microarray has revolutionized cancer research. Now, scientists can obtain a genome-wide perspective of cancer gene expression. One potential application of this technology is the discovery of novel cancer biomarkers for more accurate diagnosis and prognosis, and potentially for the earlier detection of disease or the monitoring of treatment effectiveness. Because microarray experiments generate a tremendous amount of data and because the number of laboratories generating microarray data is rapidly growing, new bioinformatics strategies that promote the maximum utilization of such data are necessary. Here, we describe a method to validate multiple microarray data sets, a Web-based cancer microarray database for biomarker discovery, and methods for integrating gene ontology annotations with microarray data to improve candidate biomarker selection.
Poly(Ethyleneimine)‐Immobilized‐Cloth Enzyme Immunoassay for the Detection ofSalmonellaLipopolysaccharide (2003)

Poly(ethyleneimine) (PEI) was immobilized on non-woven polyester cloth and examined for application on a simple, rapid and economical "cloth enzyme immunoassay (CEIA)" which was developed originally as polymyxin-CEIA for the detection of Salmonella lipopolysaccharide (LPS). PEI-cloth regardless of the PEI molecular weight, but with the amine group contents of 0.1 to approximately 0.35 meq/g immobilized either in a physisorption-like or chemisorption-like manner, adsorbed LPS rapidly, preferentially and effectively. The captured LPS was then able to be detected qualitatively and quantitatively as an antigen by enzyme immunoassay. PEI-CEIA had a detection limit for Salmonella LPS of 10 ng/ml, which was equivalent to 1.6 x 10(5) cell/ml and was ten times more sensitive than polymyxin-CEIA. It was possible to detect Salmonella LPS in the presence of a 100-fold excess of E. coli LPS. PEI-CEIA was found to be more sensitive and much easier to carry out than polymyxin-CEIA but had the same advantages as polymyxin-CEIA.
Implementing one standardized rehabilitation protocol following autologous chondrocyte implantation or microfracture in the knee results in comparable physical therapy management (2010)

Overall, the compliance post-surgery with the rehabilitation protocol was excellent and the applied rehabilitation was comparable in both treatment groups. A high amount of low-load activities post-surgery appears beneficial for the objective functional outcome.
Supplementary Data S5 from Optimizing precision medicine for breast cancer brain metastases with functional drug response assessment. (2023)

&lt;p&gt;GSEA analysis using the oncogenic, KEGG, and GOBP gene sets.&lt;/p&gt;
Preparation and Microstructure of ZnO Fine Particles by Ultrasonic Spray Pyrolysis Method. (1992)

噴霧熱分解法を用いて, Zn (NO3) 2・6H2Oの水溶液を出発原料としてZnO微粒子の生成を行った.操作条件として, キャリアーガスを窒素または空気に変えて, 反応管の設定温度, キャリアーガスの流量, 噴霧液濃度を変えて粒子生成の制御を行った結果, 粒子径が0.3～1μmのウルツ鉱型ZnO微粒子を得た.実験結果より, 管設定温度およびキャリアーガスの流量は生成粒子の結晶性に影響し, 管設定温度が高いほど, またはキャリアーガスの流量が小さいほど, 生成粒子の結晶性は向上することがわかった.ただし, キャリアーガスが空気の場合は.高い管設定温度域において結晶性は低下した.また, 噴霧液濃度は粒子径に影響し.液濃度が高いほど.生成粒子径は増大した.さらに, 生成粒子の微細構造を電子顕微鏡により観察した結果, 一次粒子径は約20～100nmのもので, 中空状の凝集粒子であることがわかり, これにより本法における粒子生成機構が推論された.
Growth of the Mongolian Gerbil, Meriones unguiculatus (1969)

Patterns of growth and development of the Mongolian gerbil, Meriones unguiculatus, were studied and compared with those of other Cricetid rodents. The gestation period was about 36 days, and litter sizes ranged from 2 to 7. The young averaged 2.57 g at birth, with tail length of 10 mm, hind foot of 9 mm, and ear of 2 mm. Weight increased linearly by a factor of 0.38 g/day. Most growth was completed by the fourth week, though all measurements were still increasing slowly after one year. Eyes opened 18 to 20 days after birth, and weaning was usually completed by the fourth week. The Mongolian gerbil, Meriones unguiculatus, is used widely as a laboratory animal, for the maintenance of certain parasites (Norman and Kagan, 1961; Leland, 1961, 1963; Lewis and Gray, 1961; Boisvenue, 1965), and in studies of water balance (Winkelman and Getz, 1962), endocrinology (Francois, Johnson, and Yong, 1966; Glenn and Gray, 1965; Thiessen, Friend, and Lindzey, 1968), and general physiology (Marston and Chang, 1964; Robinson, 1959). A study has been made of organ weight-body weight ratios (Wilber and Gilchrist, 1965), but the growth rate and patterns of development previously have not been reported. Gestation Period. The gestation period was estimated from a series of six litters born to one pair of gerbils. The least time between successive litters was 36 days. In this instance mating was observed the day the previous litter had been born, and the female refused further advances by the male. The pair was not separated at this time, however, and the gestation period should be verified later. The time intervals between the other litters were 54, 80, 45, and 56 days, respectively. Variations may be due, not only to mating success, but to the age of the previous litter, for it has been reported that gestation periods of other Cricetids are longer for lactating females (Svihla, A., 1935, 1936; Svihla, R.D., 1936). Seasonal Birth Cycle. Mongolian gerbils give birth year around in captivity. This may not be the case in wild populations, however, as evidenced by the September to November birth season for wild Meriones Transactions of the Kansas Academy of Science, Vol. 72, No. 2, 1969. Published September 17, 1969.
A data-driven medication score predicts 10-year mortality among aging adults (2020)

Health differences among the elderly and the role of medical treatments are topical issues in aging societies. We demonstrate the use of modern statistical learning methods to develop a data-driven health measure based on 21 years of pharmacy purchase and mortality data of 12,047 aging individuals. The resulting score was validated with 33,616 individuals from two fully independent datasets and it is strongly associated with all-cause mortality (HR 1.18 per point increase in score; 95% CI 1.14-1.22; p = 2.25e-16). When combined with Charlson comorbidity index, individuals with elevated medication score and comorbidity index had over six times higher risk (HR 6.30; 95% CI 3.84-10.3; AUC = 0.802) compared to individuals with a protective score profile. Alone, the medication score performs similarly to the Charlson comorbidity index and is associated with polygenic risk for coronary heart disease and type 2 diabetes.
Abstract 4890: Diffusion-weighted MRI provides an early assessment of treatment response in a murine model of metastatic prostate cancer to the bone (2011)

Abstract Ninety percent of patients with advanced prostate cancer develop metastases to the bone1. At present, there is no definitive means for assessing response to therapy, with RECIST identifying tumors in the bone as “unmeasureable”. Diffusion-weighted MRI (DW-MRI) is highly sensitive to microscopic changes in tumor tissue. Our goal is to use DW-MRI to detect and quantify changes in tumor tissue throughout therapy where the magnitude of the change could be related to the effectiveness of the treatment. Human prostate cancer (PC3) cells were implanted by direct intra-tibial injection into male SCID mice, which served as a model for prostate bone metastases. MRI experiments were performed on a 9.4T MRI. Upon identifying a tumor volume of ∼10mm3, animals were randomly distributed into 4 treatment groups: docetaxel 20 mg/kg i.p. dose once a week for 3 doses (qd7×3; N=5), fractionated radiation IR at 2 Gy/day 5x per week for 2 weeks (N=7), combined treatment (N=5) and control (N=6). Animals were imaged by DW-MRI in which the apparent diffusion coefficient was calculated from the DW images. Tumor volume and ADC measurements were acquired pre-treatment and on days 0, 1, 4, 7, and once per week after post-treatment initiation. Animals were removed from the study when the tumor reached a percent increase of 400% (5x the initial tumor volume). Group comparisons in MRI metrics were obtained using an unpaired Student t-test. Mice treated by Dox or IR had significant smaller increase in tumor volume compared to control mice. Combined treatment resulted in improved efficacy over lone therapies. This resulted in a significant decrease in tumor size. The Dox group showed an increase in ADC following the first administration and a slow decline in ADC values following day 4 post-treatment initiations regardless of additional treatments. ADC value for IR treated animals did not elevate above control until day 7. Combined treatment generated increased ADC values that were maintained throughout the treatment cycle. IR and Dox alone and in combination were effective as assessed by anatomical and DW-MRI. Those results demonstrate the potential of quantitative ADC map for assessing early response of metastatic cancer to the bone. References: 1. Carlin BI et al. Cancer. 2000;88(12):2989-2994. 2. Lee KC et al. Cancer Res. 2007;67(8):3524-3528. 3. Lee KC Neoplasia. 2007;9(12):1003-1011. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4890. doi:10.1158/1538-7445.AM2011-4890
Osteoblast-Mediated Resorption of Porous Bioactive SCPC Granules Enhances Bone Regeneration in Human Extraction Sockets (2022)

Bone graft materials are widely used in orthopedic and maxillofacial surgeries. The controlled resorbability of the graft material is essential for bone regeneration. Hydroxyapatite and biphasic calcium phosphate bone grafts have poor resorption and limited bone conductive effects. Histology analyses of bone biopsy from SCPC grafted human extraction sockets showed complete bone regeneration and graft resorption in absence of osteoclasts and macrophages. The hypothesis of the present study is that bioactive SCPC inhibits osteoclast’s activity due to the presence of resorbable silica phase in the material. Our objective is to analyze the effect of SCPC dissolution products on the resorption activity of osteoclasts. The conditioned medium was prepared by immersion of SCPC resorbable bioactive SCPC porous granules (Shefabone, Inc, USA) in cell culture medium at various ratios at 37°C for 3 days. The concentration of Si ions released from the SCPC granules into cell culture medium was measured using ICP-OES. Osteoclast precursors derived from human bone marrow were seeded on bone slices and cultured in the conditioned medium containing 10% FBS and osteoclast induction factors. Osteoclast differentiation and resorption were evaluated by TRAP staining and measurement of the volume of resorption pits on the bone slices. Mature multinuclear giant TRAP-positive osteoclasts were observed on the bone substrates after 14 days incubation in control medium containing osteoclast induction factors. In conditioned medium, the number of multinuclear TRAP-positive cells was significantly decreased as the concentration of SCPC dissolved silica increased. The dissolution of silica from SCPC into the culture medium correlates well with down regulation of osteoclast differentiation and the rapid bone regeneration in human bone defects.
Immunogenization of a murine T-cell lymphoma via transfection with interferon-gamma. (1995)

Tumor cell variants were derived from the BW5147 T-cell lymphoma that differ in major histocompatibility complex (MHC) class I antigen expression, tumorigenicity and metastatic potential. In general, increased H-2Kk expression was found to be correlated with a reduced tumorigenicity and spontaneous metastasis. CD8+ T cells were identified in the immune recognition of such variants, implicating a role for H-2Kk in the presentation of tumor-associated antigens. In the present study, H-2Kk+ BW variants were transfected with a gene encoding interferon-gamma (IFN-gamma), a potent inducer of MHC class I expression. The resulting transfectants exhibited an increased expression of H-2Kk and concomitantly an inability to generate visible tumors and a reduced metastatic capacity. Furthermore, immunization with the IFN-gamma transfectants resulted in an increased generation of cytotoxic T lymphocytes (CTLs) that lysed both the transfectants and the parental tumor cells. Based on these results, vaccinations with the IFN-gamma transfectants were performed against the parental tumor cells. The results clearly demonstrated that such vaccinations reduced significantly the tumorigenicity and metastatic capacity of the parental tumor cells. Hence, in this tumor model, IFN-gamma gene transfection provides a means to immunogenize H-2Kk+ BW tumor cells.
Surprising Coordination Geometry Differences in Ce(IV)- and Pu(IV)-Maltol Complexes (2008)

As part of a study to characterize the detailed coordination behavior of Pu(IV), single crystal X-ray diffraction structures have been determined for Pu(IV) and Ce(IV) complexes with the naturally-occurring ligand maltol (3-hydroxy-2-methyl-pyran-4-one) and its derivative bromomaltol (5-bromo-3-hydroxy-2-methyl-pyran-4-one). Although Ce(IV) is generally accepted as a structural analog for Pu(IV), and the maltol complexes of these two metals are isostructural, the corresponding bromomaltol complexes are strikingly different with respect to ligand orientation about the metal ion: All complexes exhibit trigonal dodecahedral coordination geometry but the Ce(IV)-bromomaltol complex displays an uncommon ligand arrangement not mirrored in the Pu(IV) complex, although the two metal species are generally accepted to be structural analogs.
[The effect of hyperbaric oxygen on ophthalmic artery blood velocity in patients with diabetic neuropathy]. (1997)

We investigated changes in the blood velocity of the ophthalmic artery to observe its relationship to the complication of diabetes mellitus before and after hyperbaric oxygen therapy (HBO). Color Doppler imaging (Toshiba, SSA-260A) was used. In this study, there were 7 diabetic neuropathy patients, 3 diabetes patients without neuropathy, and 7 normal subjects for control. These patients were examined before and after HBO. The patients were made to breathe 100% oxygen at 2.0 atmosphere absolute (ATA) for one hour. HBO is sometimes used for treatment of diabetic neuropathy. HBO produced an average decrease in blood velocity of 15.0 +/- 9.0 (mean +/- standard deviation) % in normal subjects, 10.7 +/- 8.6% in diabetes patients without neuropathy, and returned to the baseline level 4 hours after the conclusion of HBO. On the other hand, the blood velocity increased by about 20.6 +/- 9.5% in diabetic neuropathy patients regardless the degree of severity of diabetic retinopathy. These results suggest that the increase in the blood velocity of the ophthalmic artery after HBO in diabetic neuropathy patients could be attributed to an imbalance in autonomic nervous function.
Assessment of weak-coupling approximations on a driven two-level system under dissipation (2021)

Abstract The standard weak-coupling approximations associated to open quantum systems have been extensively used in the description of a two-level quantum system, qubit, subjected to relatively weak dissipation compared with the qubit frequency. However, recent progress in the experimental implementations of controlled quantum systems with increased levels of on-demand engineered dissipation has motivated precision studies in parameter regimes that question the validity of the approximations, especially in the presence of time-dependent drive fields. In this paper, we address the precision of weak-coupling approximations by studying a driven qubit through the numerically exact and non-perturbative method known as the stochastic Liouville–von Neumann equation with dissipation. By considering weak drive fields and a cold Ohmic environment with a high cutoff frequency, we use the Markovian Lindblad master equation as a point of comparison for the SLED method and study the influence of the bath-induced energy shift on the qubit dynamics. We also propose a metric that may be used in experiments to map the regime of validity of the Lindblad equation in predicting the steady state of the driven qubit. In addition, we study signatures of the well-known Mollow triplet and observe its meltdown owing to dissipation in an experimentally feasible parameter regime of circuit electrodynamics. Besides shedding light on the practical limitations of the Lindblad equation, we expect our results to inspire future experimental research on engineered open quantum systems, the accurate modeling of which may benefit from non-perturbative methods.