gebhart/patrepeval huggingface dataset:
Comparison of Rates and Kinetic Isotope Effects Using PEG-Modified Variants and Glycoforms of Glucose Oxidase:  The Relationship of Modification of the Protein Envelope to C−H Activation and Tunneling (2002)

An earlier investigation of the temperature dependencies of rates and kinetic isotope effects (KIEs) in glucose oxidase (GO) used variants that differed in the extent of glycosylation at the surface of the protein. Kohen et al. [Kohen, A., Jonsson, T., and Klinman, J. P. (1997) Biochemistry 36, 2603-2611] presented evidence that the KIE on the Arrhenius prefactor varied as a function of protein modification, concluding that the degree of hydrogen tunneling at the active site was dependent on changes in mass at the surface. We now examine GO proteins containing polyethylene glycol (PEG) at their surface and a more extensively glycosylated form of GO, to distinguish simple mass effects from other sources of altered catalytic behavior. One PEG variant was created by modifying deglycosylated GO with short PEG chains (average of 350 Da each), while another contained a smaller number of long PEG chains (average of 5000 Da each). The light (146 kDa) and heavy (211 kDa) PEG variants and the hyperglycosylated variant display isotope effects on the Arrhenius prefactor that are similar (A(D)/A(T) = 0.55-0.62), while the unperturbed wild-type GO (WT-GO) is found to have an A(D)/A(T) that is reassessed as being close to unity. It appears that any modification of the protein surface away from that of the wild type gives rise to altered behavior for hydrogen transfer in the active site. We have also compared the effect of enthalpies of activation on both k(cat)/K(M) and k(cat) for the variants, introducing a new method to extract the k(cat)/K(M) rate constant and enthalpy of activation for the tritiated substrate from competitive KIE experiments. We find similar trends in Delta H(++) for both competitive and noncompetitive parameters and a smaller trend in k(cat) than reported earlier. Correlations are observed between A(D)/A(T) and both the enthalpies of activation and the thermal melt temperatures (T(M)) of the GO isoforms. In addition to the present study, there are now a number of examples where a perturbation of enzyme structure away from that of the wild type causes the observed KIE to become more temperature-dependent. The implications of these findings are discussed in the context of hydrogen tunneling and the relationship of protein structure and dynamics to this process.
Rhodococcus zopfii sp. nov., a Toxicant-Degrading Bacterium (1994)

A toluene-degrading bacterial strain isolated from bioreactors was identified as a member of the genus Rhodococcus on the basis of the following characteristics: meso-diaminopimelic acid, arabinose, galactose, and glucose are the diagnostic cellular sugars; the mycolic acids contain 33 to 36 carbon atoms; and the formation of a branching mycelium is followed by marked fragmentation of the mycelium into irregular rod-shaped to coccoid units. DNA-DNA hybridization analyses performed with type strains of Rhodococcus species showed that this strain is less than 70% related to other species that have similar phenotypic characteristics. On the basis of these findings, we propose that this strain should be described as a new species, Rhodococcus zopfii, in honor of Wilhelm Friedrich Zopf. The type strain is strain T1.
Human fetal pancreatic islet-like structures as source material to treat type 1 diabetes (2013)

The incidence of type 1 diabetes is increasing worldwide. Current therapy continues to be suboptimal. An exciting therapeutic advance in the short term is closed loop technology development and application. However, cell and tissue therapy continues to be an unmet need for the disorder. Human islets isolated from deceased donors will be clinically available to treat type 1 diabetes within the next 1 to 2 years. Other approaches such as xenotransplantation and islet products derived from human embryonic stem cells and induced pluripotent stem cells are currently being pursued. The current commentary provides context and discusses future endeavors for transplantation of islet-like structures derived from fetal pancreas.
Sequence composition and genome organization of maize (2004)

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome approximately 80% the size of the human genome. To gain global insight into the organization of its genome, we have sequenced the ends of large insert clones, yielding a cumulative length of one-eighth of the genome with a DNA sequence read every 6.2 kb, thereby describing a large percentage of the genes and transposable elements of maize in an unbiased approach. Based on the accumulative 307 Mb of sequence, repeat sequences occupy 58% and genic regions occupy 7.5%. A conservative estimate predicts approximately 59,000 genes, which is higher than in any other organism sequenced so far. Because the sequences are derived from bacterial artificial chromosome clones, which are ordered in overlapping bins, tagged genes are also ordered along continuous chromosomal segments. Based on this positional information, roughly one-third of the genes appear to consist of tandemly arrayed gene families. Although the ancestor of maize arose by tetraploidization, fewer than half of the genes appear to be present in two orthologous copies, indicating that the maize genome has undergone significant gene loss since the duplication event.
Organic volatile sulfur in lakes of the Canadian Shield and its loss to the atmosphere (1991)

Identities, concentrations, and fluxes of volatile sulfur compounds (VSCs) were determined in 11 lakes in northwestern Ontario. Carbonyl sulfide (COS: up to 1.1 nM) and dimethyl sulfide (DMS: up to 11 nM) were present in surface waters during most of the ice‐free season. Depth profiles showed accumulations below the mixed layer of methane thiol (MSH), DMS, and dimethyl disulfide (DMDS). There was no effect of low pH or increased [SO 4 2 − ] (from 2.4 to 12.3 mg liter −1 ) on the concentrations and identities of surface‐water VSCs. Accumulation of DMS below the mixed layer was 9 × higher in an acidified system, however, when compared to an unacidified reference lake. Estimates of flux from two stratified lakes indicated that volatilization was not an important sulfur loss mechanism compared to others such as sedimentary SO 4 2 reduction. Concentrations of MSH, DMS, and DMDS in shallow Lakes 114 and 303 were often 5–30 × higher than in any other lake studied, and the flux from Lake 114 was ∼0.96–1.6 × the estimated oceanic DMS flux per unit of area. On a regional basis, in areas where SO 4 2− in precipitation is low, export of VSCs to the atmosphere from shallow lakes and bog pools may be significant compared to sulfur inputs through precipitation.
Properties of the Log-Normal Particle Size Distribution (1994)

Abstract This note presents analytical relationships that connect the parameters of any moment of the log-normal distribution to those of any other, allowing one to harmonize experimental data derived with varying particle sensors. They also make possible calculating essential aerosol parameters that may not be amenable to direct measurements.
Berek & Hacker's Gynecologic Oncology, 7e (2010)

Section I: GENERAL PRINCIPLES Chapter 1: Biology and Genetics Chapter 2: Biologic, Targeted and Immunotherapy Chapter 3: Chemotherapy Chapter 4: Radiation Therapy Chapter 5: Pathology Chapter 6: Epidemiology and Biostatistics Chapter 7: Tumor Markers and Screening Section II: DISEASE SITES Chapter 8: Preinvasive Disease Chapter 9: Cervical Cancer Chapter 10: Uterine Cancer Chapter 11: Epithelial Ovarian, Fallopian Tube and Peritoneal Cancer Chapter 12: Germ Cell and Other Nonepithelial Ovarian Cancers Chapter 13: Vulvar Cancer Chapter 14: Vaginal Cancer Chapter 15: Gestational Trophoblastic Neoplasia Chapter 16: Breast Disease Chapter 17: Cancer in Pregnancy Section III: MEDICAL AND SURGICAL TOPICS Chapter 18: Preoperative Evaluation, Medical Management, and Critical Care Chapter 19: Nutritional Therapy Chapter 20: Surgical Techniques Chapter 21: Laparoscopy and Robotics Chapter 22: Pelvic Exenteration Section IV: QUALITY OF LIFE Chapter 23: Communications Skills Chapter 24: Symptom Relief and Palliative Care Chapter 25: Psychological Issues Index
Energy transfer between laser beams due to recording of optical axis gratings in liquid crystals (2006)

We have studied two-beam-coupling processes related to the generation of optical axis gratings in liquid crystals (LCs) due to the electromagnetic torque acting on the orientation of LCs in superimposed laser beams with spatially modulated polarization. Such gratings result in efficient coupling between the laser beams controlled by the frequency shift introduced between the beams at infrasound frequencies. Larger than 80% efficiency of energy transfer from a pump to a signal beam is reported at power density levels of the laser beams at 1-10 kW/cm2. The distinction between pump and signal beams is relative, since the sign of the frequency shift rather than the power ratio between the beams determines the direction of energy transfer. The experiments were performed for radiation at a 1.06 μm wavelength; high optical nonlinearity and low absorption make LCs suitable for use in visible and near-IR spectra, particularly in high-power laser systems. We have characterized the main fundamental features of the process of recording dynamic orientation gratings, plotting the gain spectra for several LCs and verifying the good quality of the amplified signal beam even for a strongly distorted pump. The obtained results set the groundwork for a variety of novel opportunities and applications that include combining high-power laser beams and wavelength division multiplexing at an ultranarrow interval of frequencies of the order of 1-100 Hz.
Environment-to-phenotype mapping and adaptation strategies in varying environments (2019)

Biological organisms exhibit diverse strategies for adapting to varying environments. For example, a population of organisms may express the same phenotype in all environments ("unvarying strategy") or follow environmental cues and express alternative phenotypes to match the environment ("tracking strategy"), or diversify into coexisting phenotypes to cope with environmental uncertainty ("bet-hedging strategy"). We introduce a general framework for studying how organisms respond to environmental variations, which models an adaptation strategy by an abstract mapping from environmental cues to phenotypic traits. Depending on the accuracy of environmental cues and the strength of natural selection, we find different adaptation strategies represented by mappings that maximize the long-term growth rate of a population. The previously studied strategies emerge as special cases of our model: The tracking strategy is favorable when environmental cues are accurate, whereas when cues are noisy, organisms can either use an unvarying strategy or, remarkably, use the uninformative cue as a source of randomness to bet hedge. Our model of the environment-to-phenotype mapping is based on a network with hidden units; the performance of the strategies is shown to rely on having a high-dimensional internal representation, which can even be random.
Effect of a HF–HF/HCl Treatment of 26 Coals on Their Composition and Pyrolysis Behavior (2019)

Coals contain many types of minerals. The minerals' effect on coal pyrolysis has been studied extensively in the literature by comparing only a few raw coals (R-coals) with the corresponding acid-treated coals. This paper studies an acid treatment of 26 coals from lignite to anthracite and compares the elemental composition and pyrolysis behavior of the acid-treated demineralized coals (D-coals) with the R-coals. The acid treatment involved leaching the coals with a HF solution and then with a mixed HF/HClsolution in air at 70 °C, and the pyrolysis was carried out in a temperature range of 120–900 °C in a thermal gravimetric analysis coupled online with a mass spectrometer. The characteristic parameters of the differential mass–loss curves (differential thermal gravimetric, DTG) and the subpeaks decoupled from the DTG curves are compared and discussed. It is found that the acid treatment not only removed most of the minerals from the coals but also reduced the coals' carbon content, increased their oxygen content, and altered their organic structure, leading to reduced mass loss in pyrolysis, especially for mid-rank coals. Some minerals removed by the acid treatment promote the coal pyrolysis in the temperature range of 400–600 °C corresponding mainly to the cleavage of Cal–Cal and Car–Cal bonds as well as to the decomposition of crystal water. Some of the minerals inhibited the condensation of the aromatic structure at temperatures higher than 700 °C. The reduced carbon content and increased oxygen content of D-coals are attributed to the conversion of carboxylates to carboxylic acid which promoted the pyrolysis at temperatures lower than 300 °C. The composition and pyrolysis behavior of anthracites are not significantly affected by the acid treatment.
A Ralstonia solanacearum effector targets TGA transcription factors to subvert salicylic acid signaling (2022)

The bacterial pathogen Ralstonia solanacearum causes wilt disease on Arabidopsis thaliana and tomato (Solanum lycopersicum). This pathogen uses type III effectors to inhibit the plant immune system; however, how individual effectors interfere with plant immune responses, including transcriptional reprograming, remain elusive. Here, we show that the type III effector RipAB targets Arabidopsis TGACG SEQUENCE-SPECIFIC BINDING PROTEIN (TGA) transcription factors, the central regulators of plant immune gene regulation, via physical interaction in the nucleus to dampen immune responses. RipAB was required for R. solanacearum virulence on wild-type tomato and Arabidopsis but not Arabidopsis tga1 tga4 and tga2 tga5 tga6 mutants. Stable expression of RipAB in Arabidopsis suppressed the pathogen-associated molecular pattern-triggered reactive oxygen species (ROS) burst and immune gene induction as well as salicylic acid (SA) regulons including RBOHD and RBOHF, responsible for ROS production, all of which were phenocopied by the tga1 tga4 and tga2 tga5 tga6 mutants. We found that TGAs directly activate RBOHD and RBOHF expression and that RipAB inhibits this through interfering with the recruitment of RNA polymerase II. These results suggest that TGAs are the bona fide and major virulence targets of RipAB, which disrupts SA signaling by inhibiting TGA activity to achieve successful infection.
Oxidative stress induced heat shock factor phosphorylation and HSF-dependent activation of yeast metallothionein gene transcription. (1996)

Metallothioneins (MTs) are a class of low-molecular-weight, cysteine- rich metal-binding proteins that function in metal detoxification and oxidative stress protection. We demonstrate that transcription of the Saccharomyces cerevisiae MT gene CUP1 is strongly activated by the superoxide anion generator menadione. This activation is exacerbated in a strain lacking the gene encoding Co, Zn superoxide dismutase (SOD1). CUP1 transcriptional activation by oxidative stress is dependent on a functional CUP1 promoter heat shock element (HSE) and the carboxy-terminal trans-activation domain of heat shock transcription factor (HSF). Furthermore, protection against oxidative stress conferred by CUP1 in a (sod1)delta strain requires HSF-mediated CUP1 transcription. Although in response to heat, HSF-mediated CUP1 transcription and HSF phosphorylation are transient, both CUP1 gene expression and HSF phosphorylation are sustained in response to oxidative stress. Moreover, the patterns of tryptic phosphopeptides resolved from HSF derived from cells subjected to heat shock or oxidative stress are distinct. These results demonstrate that transcription of the S. cerevisiae metallothionein gene under conditions of oxidative stress is mediated by HSF and that in response to distinct activation stimuli, HSF is differentially phosphorylated in a manner that parallels metallothionein gene transcription.
EGFR Mutation Positive Stage IV Non-Small-Cell Lung Cancer: Treatment Beyond Progression (2014)

Non-small-cell lung cancer (NSCLC) is the leading cause of death from cancer for both men and women. Chemotherapy is the mainstay of treatment in advanced disease, but is only marginally effective. In about 30% of patients with advanced NSCLC in East Asia and in 10-15% in Western countries, epidermal growth factor receptor (EGFR) mutations are found. In this population, first-line treatment with the tyrosine kinase inhibitors (TKIs) erlotinib, gefitinib, or afatinib is recommended. The treatment beyond progression is less well-defined. In this paper, we present three patients, EGFR mutation positive, with local progression after an initial treatment with TKI. These patients were treated with local radiotherapy. TKI was temporarily stopped and restarted after radiotherapy. We give an overview of the literature and discuss the different treatment options in case of progression after TKI: TKI continuation with or without chemotherapy, TKI continuation with local therapy, alternative dosing or switch to next-generation TKI or combination therapy. There are different options for treatment beyond progression in EGFR mutation positive metastatic NSCLC, but the optimal strategy is still to be defined. Further research on this topic is ongoing.
Cover Picture: Dipole Effects on Electron Transfer are Enormous (Angew. Chem. Int. Ed. 38/2018) (2018)

The electric dipole of a donor strongly affects the electron transfer (ET) to a photoexcited acceptor. In their Communication on page 12365 ff., G. J. O. Beran, D. T. Gryko, V. I. Vullev, and co-workers show that lowering the polarity of the medium can allow an electric dipole to enhance the rates of electron-transfer processes along it, while completely suppressing those occurring against it. Favorable dipole orientation makes ET possible even in lipophilic media. The electric dipole of a donor strongly affects the electron transfer (ET) to a photoexcited acceptor. In their Communication on page 12365 ff., G. J. O. Beran, D. T. Gryko, V. I. Vullev, and co-workers show that lowering the polarity of the medium can allow an electric dipole to enhance the rates of electron-transfer processes along it, while completely suppressing those occurring against it. Favorable dipole orientation makes ET possible even in lipophilic media. Biocatalysis Electrocatalysis Protein Labeling
Nanowire Crossbar Logic and Standard Cell-Based Integration (2009)

Nanowire crossbar is one of the most promising circuit solutions for nanoelectronics. However, it is still unclear whether or how they can be competitive in implementing logic circuits, as compared to their MOSFET counterparts. We analyze nanowire crossbars in area, speed, and power, in comparison with their MOSFET counterparts. We show nanowire crossbars do not scale well in terms of logic density and speed. To achieve performance close to their MOSFET counterparts, crossbar circuits need faster field-effect transistors (FETs) to compensate the high resistance of nanowires. Motivated by the analysis and comparative study, we propose a crossbar cells design based on judicious use of silicon nanowires. The crossbar cell is compatible with the conventional MOSFET fabrication and design methodologies, in particular, standard cell-based integrated circuit design. We evaluate logic circuits synthesized with crossbar cells and MOSFET cells based on the MCNC91 benchmark. The results show that crossbar cells can provide a density advantage of more than four times over the traditional MOSFET circuits with the same process technology, while achieving close performance and consuming less than one third power.
Elucidating Mechanisms of Farnesyltransferase Inhibitor Action and Resistance in Breast Cancer by Bioluminescence Imaging (2008)

Abstract : Prenyltransferase inhibitors (FTIs & GGTIs) block post-translational processing of Ras-like GTPases that have key roles in breast cancer. However, FTIs have yet to be used widely in breast cancer therapy because it is not yet possible to identify patients likely to be FTI-sensitive or to use combinatorial therapy to broaden the spectrum of patients that respond to FTIs. A new lentiviral-based prenylation responsive bioluminescence reporter system has been constructed and validated in human breast cancer cell lines. Our strategy should offer the opportunity to visualize over time the action of FTIs and GGTIs toward specific, biologically relevant prenylation-dependent proteins in tumors of living animals in vivo.
Automated Segmentation and Connectivity Analysis for Normal Pressure Hydrocephalus (2022)

<i>Objective and Impact Statement</i>. We propose an automated method of predicting Normal Pressure Hydrocephalus (NPH) from CT scans. A deep convolutional network segments regions of interest from the scans. These regions are then combined with MRI information to predict NPH. To our knowledge, this is the first method which automatically predicts NPH from CT scans and incorporates diffusion tractography information for prediction. <i>Introduction</i>. Due to their low cost and high versatility, CT scans are often used in NPH diagnosis. No well-defined and effective protocol currently exists for analysis of CT scans for NPH. Evans' index, an approximation of the ventricle to brain volume using one 2D image slice, has been proposed but is not robust. The proposed approach is an effective way to quantify regions of interest and offers a computational method for predicting NPH. <i>Methods</i>. We propose a novel method to predict NPH by combining regions of interest segmented from CT scans with connectome data to compute features which capture the impact of enlarged ventricles by excluding fiber tracts passing through these regions. The segmentation and network features are used to train a model for NPH prediction. <i>Results</i>. Our method outperforms the current state-of-the-art by 9 precision points and 29 recall points. Our segmentation model outperforms the current state-of-the-art in segmenting the ventricle, gray-white matter, and subarachnoid space in CT scans. <i>Conclusion</i>. Our experimental results demonstrate that fast and accurate volumetric segmentation of CT brain scans can help improve the NPH diagnosis process, and network properties can increase NPH prediction accuracy.
Statistical analysis of timeseries data reveals changes in 3D segmental coordination of balance in response to prosthetic ankle power on ramps (2019)

Active ankle-foot prostheses generate mechanical power during the push-off phase of gait, which can offer advantages over passive prostheses. However, these benefits manifest primarily in joint kinetics (e.g., joint work) and energetics (e.g., metabolic cost) rather than balance (whole-body angular momentum, H), and are typically constrained to push-off. The purpose of this study was to analyze differences between active and passive prostheses and non-amputees in coordination of balance throughout gait on ramps. We used Statistical Parametric Mapping (SPM) to analyze time-series contributions of body segments (arms, legs, trunk) to three-dimensional H on uphill, downhill, and level grades. The trunk and prosthetic-side leg contributions to H at toe-off when using the active prosthesis were more similar to non-amputees compared to using a passive prosthesis. However, using either a passive or active prosthesis was different compared to non-amputees in trunk contributions to sagittal-plane H during mid-stance and transverse-plane H at toe-off. The intact side of the body was unaffected by prosthesis type. In contrast to clinical balance assessments (e.g., single-leg standing, functional reach), our analysis identifies significant changes in the mechanics of segmental coordination of balance during specific portions of the gait cycle, providing valuable biofeedback for targeted gait retraining.