gebhart/patrepeval huggingface dataset:
A re-evaluation of the crystal structure of chloromuconate cycloisomerase (1996)

It is shown here that the reported 3 A crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus [Hoier, Schlömann, Hammer, Glusker, Carrell, Goldman, Stezowski & Heinemann (1994). Acta Cryst. D50, 75-84] was refined in the incorrect space group I4. In addition, a stretch of about 25 residues near the N-terminus is out-of-register with the density in the original structure. From the coordinates and structure factors deposited in the Protein Data Bank (PDB), it was possible to determine the correct space group to be I422. The structure was then re-refined, using the original data reduced to I422, to a crystallographic free R factor of 0.264 at 3 A resolution (conventional R factor 0.189). With conservative refinement and rebuilding methods, the errors in the chain tracing could be identified and remedied. Since the two molecules per asymmetric unit in the original structure are actually related by crystallographic symmetry, the observed differences between them are artefacts. In particular, the differences between, and peculiarities of the metal-binding sites are unreal. This case shows the dangers of crystallographic refinement in cases with unfavourable data-to-parameter ratios, and the importance of reducing the number of parameters in such cases to prevent gross errors (for instance, by using NCS constraints). It also demonstrates how the evaluation and monitoring of model quality during the entire refinement and rebuilding process can be used to detect and remedy serious errors. Finally, it presents a strong case in favour of depositing not only model coordinates, but also experimental data (preferably, both merged and unmerged data).
A Review of the Technology, Training, and Assessment Methods for the First Real-Time AI-Enhanced Medical Device for Endoscopy (2023)

Artificial intelligence (AI) has the potential to assist in endoscopy and improve decision making, particularly in situations where humans may make inconsistent judgments. The performance assessment of the medical devices operating in this context is a complex combination of bench tests, randomized controlled trials, and studies on the interaction between physicians and AI. We review the scientific evidence published about GI Genius, the first AI-powered medical device for colonoscopy to enter the market, and the device that is most widely tested by the scientific community. We provide an overview of its technical architecture, AI training and testing strategies, and regulatory path. In addition, we discuss the strengths and limitations of the current platform and its potential impact on clinical practice. The details of the algorithm architecture and the data that were used to train the AI device have been disclosed to the scientific community in the pursuit of a transparent AI. Overall, the first AI-enabled medical device for real-time video analysis represents a significant advancement in the use of AI for endoscopies and has the potential to improve the accuracy and efficiency of colonoscopy procedures.
Resolution of GC-MS Data of Complex PAC Mixtures and Regression Modeling of Mutagenicity by PLS (2001)

The present work describes a strategy to predict the mutagenicity of very complex mixtures of polycyclic aromatic compounds (PAC) from gas chromatography-mass spectrometry (GC-MS) patterns of the mixtures, each containing 260 compounds on average. The mixtures, 13 organic extracts of exhaust particles, were characterized by full scan GC-MS. The data were resolved into peaks and spectra for individual compounds by an automated curve resolution procedure. Similarity between spectra was evaluated for peaks that appeared within a time interval of 4 min, using a similarity index of 0.8 to ascertain that the same compound was represented by the same variable name (retention time) in all samples. The resolved chromatograms were integrated, resulting in a predictor matrix of size 13 x 721, which was used as input to a multivariate regression model. Partial least-squares projections to latent structures (PLS) were used to correlate the GC-MS chromatograms to mutagenicity as measured in the Ames Salmonella assay. The best model (high r2 and Q2) was obtained with 52 variables. These variables covary with the observed mutagenicity, and may subsequently be identified chemically. Furthermore, the regression model can be used to predict mutagenicity from GC-MS chromatograms of other organic extracts.
Comparison of Minus Power Anterior Chamber Intraocular Lenses and Myopic Epikeratoplasty in Phakic Eyes (1990)

We performed a retrospective study of two sequential series of operations designed to correct high myopia in phakic eyes. The first series consisted of 21 eyes with refractive error ranging from -11.00 diopters to -21.00 D (mean -16.9 D). They received a commercially prepared, lyophilized, myopic epikeratoplasty lenticule sutured into a circular keratectomy. Seven lenticules had to be removed within the first year because of poor refractive results, corneal ulceration, or melting. The nine eyes followed from 12 to 24 months after surgery demonstrated residual refractive errors from +4.00 D to -11.25 D. We also studied an initial series of 41 eyes with preoperative myopia ranging from -9.00 D to -35.00 D (mean -15.00 D) that received a minus power anterior chamber intraocular lens. The lens had an open loop design with an anterior vault, four point angle fixation, and an optic diameter of 4.5 mm. Recovery of visual acuity was faster with the intraocular lens than with epikeratoplasty. Three intraocular lenses were removed; two because they were the wrong size and one because it was the wrong power. Two of the lenses were replaced with acceptable results. Of the 34 eyes followed for 12 months, all had a residual refractive error within +/- 2.00 D of emmetropia. During the short-term follow-up, no elevated intraocular pressure, cataract formation, or excessive endothelial damage was observed. We concluded that anterior chamber minus power intraocular lenses gave more rapid and predictable optical correction in high myopic eyes than did myopic epikeratoplasty. Longer follow-up is required before conclusions can be reached about the safety of these intraocular lenses.
Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses (2015)

Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human coronaviruses. Analytical and clinical evaluations showed their noninferiority to a commercial multiplex PCR test for the detection of these coronaviruses.
Honors Banquet Awardees (2002)

Raymond G. LaPlaca '83, a partner at Knight, Manzi, Nussbaum & LaPlaca believes in giving back to the communities that have nurtured him along the way. A partner with Brown, Goldstein & Levy, Andrew D. Levy '81 believes that having a license to practice law carries with it the responsibility of giving something back. (article continued on page 66 of JD. See link to "Continuation of Honors Banquet Awardees.")
Two-Dimensional Graphene Nanoribbons (2008)

A new synthetic strategy toward novel linear two-dimensional graphene nanoribbons up to 12 nm has been established. The nanoribbons are characterized by MS, UV/vis, and scanning tunneling microscopy (STM). Various microscopic studies of these novel structures showed a high tendency to self-assemble.
A novel high resolution, wide swath SAR system (2002)

A novel SAR system architecture is presented. It allows to combine a high azimuth resolution with a wide imaged swath width. The architecture and the required on board signal processing is described. Finally two examples systems and their image performance are presented.
Cavernous Nerve Injury Using Rodent Animal Models (2008)

Various models of CN injury have been applied successfully and offer insights regarding erectile function recovery effects.
PRESSURE-DENSITY RELATIONSHIPS OF CHOPPED SWEET SORGHUM (1990)

ABSTRACT Physical characteristics of chopped sweet sorghum relating to leaching bed and silo design were determined: pressure/density and depth/density relationships, porosity, and saturation density. Results are compared with published values for com silage.
Continuous-Wave and Time-Resolved Optically Detected Magnetic Resonance Studies of Nonetched/Etched InP Nanocrystals (2002)

The low temperature photoluminescence spectrum of InP nanocrystals (NCs) is composed of a near band-edge exciton and a defect emission band at lower energies. The present study characterized the defect emission utilizing an optically detected magnetic resonance spectroscopy (ODMR) both in continuous-wave and time-resolved modes. The continuous-wave ODMR spectra were measured as a function of the laser power, the microwave power, the microwave modulation frequencies, and of the light polarization. The results showed that the defect emission originated from the trap-to-band luminescence of a weakly coupled electron−hole pair, when the electron is trapped at a phosphorus vacancy, Vp (with angular momention of F = 1/2), while the hole is located at the valence band (with F = 3/2). Spin Hamiltonian simulations of the ODMR lineshape, including hyperfine interactions, revealed that the nonetched samples are dominated by Vp at the surface with two adjacent indium atoms. While treatment with hydrogen floride acid eliminates the surface defects, it leaves behind a small percent of Vp at the core of the NCs, with four indium atoms next neighbors at the vertexes of a tetrahedral site. The time-resolved ODMR measurements further distinguished between radiative and nonradiative processes and followed the spin dynamics at the excited state. Kinetic simulations of the PL intensity response to a microwave square wave modulation indicated that the spin−lattice relaxation time and the radiative lifetime of the weakly coupled electron−hole pair are in the microseconds regime.
Automated routing protocol selection in mobile ad hoc networks (2007)

Many protocols exist for supporting routing in mobile ad hoc networks (MANETs). Selecting a particular protocol for an application or deployment environment involves evaluating many complex inter-dependent tradeoffs and can be an overwhelming task for an application designer. However, this decision can have a significant impact on the success of a system in terms of performance, cost, and responsiveness. This paper introduces a design tool that automates this evaluation process by controlling for environmental and usage properties of an intended deployment. This provides the foundation for a highly adaptive protocol suite that lever-ages the relative benefits of competing communication paradigms.
Construction of Quaternary Carbon Stereocenter of α-Tertiary Amine through Remote C–H Functionalization of Tris Derivatives: Enantioselective Total Synthesis of Myriocin (2019)

We describe the development of a strategy for the construction of the quaternary carbon stereocenter of α-tertiary amines. This strategy highlights a site-selective C-H functionalization involving an alkoxy-radical-triggered 1,5-hydrogen transfer (1,5-HAT) reaction of a conformationally fixed spiro-compound derived from trishydroxymethylaminomethane (Tris). The utilization of this strategy enabled an enantioselective total synthesis of myriocin, a naturally occurring sphingosine analog that displays potent immunosuppressive activity.
Adaptive Transform Coefficient Scan for H.264 Intra Coding (2007)

This paper presents an adaptive transform coefficient scan method that effectively improves intra coding efficiency of H.264. Instead of applying one zig-zag scan to all transform blocks, the proposed method applies a field scan to a horizontally predicted block, a horizontal scan to a vertically predicted block, and a zig-zag scan to blocks predicted in other prediction modes. Experiments based on JM9.6 were performed using only intra coding. Results of the experiments show that the proposed method yields an average PSNR enhancement of 0.16 dB and a maximum PSNR enhancement of 0.31 dB over the current H.264 using zig-zag scan.
White matter diffusion alterations precede symptom onset in autosomal dominant Alzheimer’s disease (2018)

White matter alterations are present in the majority of patients with Alzheimer's disease type dementia. However, the spatiotemporal pattern of white matter changes preceding dementia symptoms in Alzheimer's disease remains unclear, largely due to the inherent diagnostic uncertainty in the preclinical phase and increased risk of confounding age-related vascular disease and stroke in late-onset Alzheimer's disease. In early-onset autosomal-dominantly inherited Alzheimer's disease, participants are destined to develop dementia, which provides the opportunity to assess brain changes years before the onset of symptoms, and in the absence of ageing-related vascular disease. Here, we assessed mean diffusivity alterations in the white matter in 64 mutation carriers compared to 45 non-carrier family non-carriers. Using tract-based spatial statistics, we mapped the interaction of mutation status by estimated years from symptom onset on mean diffusivity. For major atlas-derived fibre tracts, we determined the earliest time point at which abnormal mean diffusivity changes in the mutation carriers were detectable. Lastly, we assessed the association between mean diffusivity and cerebrospinal fluid biomarkers of amyloid, tau, phosphorylated-tau, and soluble TREM2, i.e. a marker of microglia activity. Results showed a significant interaction of mutations status by estimated years from symptom onset, i.e. a stronger increase of mean diffusivity, within the posterior parietal and medial frontal white matter in mutation carriers compared with non-carriers. The earliest increase of mean diffusivity was observed in the forceps major, forceps minor and long projecting fibres-many connecting default mode network regions-between 5 to 10 years before estimated symptom onset. Higher mean diffusivity in fibre tracts was associated with lower grey matter volume in the tracts' projection zones. Global mean diffusivity was correlated with lower cerebrospinal fluid levels of amyloid-β1-42 but higher levels of tau, phosphorylated-tau and soluble TREM2. Together, these results suggest that regionally selective white matter degeneration occurs years before the estimated symptom onset. Such white matter alterations are associated with primary Alzheimer's disease pathology and microglia activity in the brain.
Surface charge modulation of rifampicin-loaded PLA nanoparticles to improve antibiotic delivery in Staphylococcus aureus biofilms (2021)

Correlating the carrier retention capacity in biofilms with the treatment efficacy, positively charged rifampicin-loaded PLA nanoparticles are therefore proposed as an adapted and promising approach to improve antibiotic delivery in S. aureus biofilms.
Geometrical optics limit of stochastic electromagnetic fields (2008)

A method is described which elucidates propagation of an electromagnetic field generated by a stochastic, electromagnetic source within the short wavelength limit. The results can be used to determine statistical properties of fields using ray tracing methods.
Inflammation in muscular dystrophy and the beneficial effects of non‐steroidal anti‐inflammatory drugs (2012)

NSAIDs have a beneficial effect on mdx muscle morphology, pointing to a crucial role of inflammation in the progression of DMD.
Long-term Outcome of Transient, Uncomplicated In-Laboratory Coronary Artery Closure (1995)

Transient, uncomplicated in-laboratory vessel closure per se does not have an adverse long-term effect. However, a concomitant elevation of postprocedure cardiac enzymes has an important and significant adverse effect on long-term outcome. This study suggests that periprocedural creatine kinase isoenzyme determination in patients experiencing in-laboratory coronary closure has important prognostic implications.
CD46 Expression is an Unfavorable Prognostic Factor in Breast Cancer Cases (2011)

The membrane cofactor protein, CD46 represents a complement inhibitor, which protects autologous cells from complement-mediated cytotoxicity. On tumor cells, CD46 may exhibit the potential to protect them from immune responses of the host. The present study aimed at evaluation of prognostic significance of CD46 expression in breast cancers. The analyses were performed on 70 samples of breast cancer. Immunohistochemical reactions were performed on paraffin sections of studied tumors using monoclonal antibodies directed against CD46. Results of the immunohistochemical reactions and of clinical observations were subjected to statistical analysis. Multivariate analysis showed that expression of CD46 and involvement of lymph nodes represent independent risk factors for disease-free survival and overall survival. Kaplan-Meier analysis showed that patients with tumors negative for CD46 have an increased progression-free time and overall survival time as compared with patients with the CD46-positive tumors. The study demonstrates that breast cancers manifest CD46 expression and that it is linked to a less favorable prognosis.
Denervation-induced decrease in mitochondrial calcium transport in rat hippocampus (1983)

Calcium accumulation by mitochondria and the activity and in vitro phosphorylation of pyruvate dehydrogenase were measured in control and partially denervated hippocampus. Calcium uptake was measured with a calcium-sensitive electrode and 45Ca2+ accumulation; both methods indicated that lesions of the entorhinal cortex produced a sizable reduction of calcium transport when mitochondria were fueled with pyruvate while much smaller changes were observed using succinate or ATP as energy sources. The decrease in calcium transport was evident by 24 hr after the lesion and was still present 6 months later. Synaptic and nonsynaptic mitochondria were similarly affected by the lesions. The activity and in vitro phosphorylation of pyruvate dehydrogenase were also significantly reduced following lesions of the entorhinal cortex, suggesting that denervation altered the endogenous state of phosphorylation of the mitochondrial enzyme. Commissural lesions but not septal lesions also resulted in a decrease in mitochondrial calcium transport when mitochondria were fueled with pyruvate. These findings suggest that denervation disturbs mitochondrial regulation of free calcium via an action on enzymes which regulate pyruvate dehydrogenase phosphorylation and activity. The potential relationship of this effect to degenerative changes associated with deafferentation and certain disease states is discussed.
Catalytic dehydrogenation of iminodibenzyl to iminostilbene on Mn2O3-SnO2. (1982)

Catalytic dehydrogenation of iminodibenzyl to iminostilbene was carried out at 550°C on a binary oxide system of Mn2O3-SnO2. Maximum activity was observed at an Mn2O3-SnO2 ratio of 8 : 2 ; conversion was 40%, selectivity 82%. Mn2O3-SnO2 catalyst dispersed on MgO and modified with K2CO3 gave 80-90% conversion and 82-88% selectivity. The relation between activity and the physical properties of catalysts was studied.
Differential localization of PD-L1 and Akt-1 involvement in radioresistant and radiosensitive cell lines of head and neck squamous cell carcinoma (2019)

Immunotherapy by blockade of the PD-1/PD-L1 checkpoint demonstrated amazing tumor response in advanced cancer patients including head and neck squamous cell carcinoma (HNSCC). However, the majority of HNSCC patients still show little improvement or even hyperprogression. Irradiation is currently investigated as synergistic treatment modality to immunotherapy as it increases the number of T-cells thereby enhancing efficacy of immunotherapy. Apart from this immunogenic context a growing amount of data indicates that PD-L1 also plays an intrinsic role in cancer cells by regulating different cellular functions like cell proliferation or migration. Here, we demonstrate opposing membrane localization of PD-L1 in vital and apoptotic cell populations of radioresistant (RR) and radiosensitive (RS) HNSCC cell lines up to 72 h after irradiation using flow cytometry. Moreover, strong PD-L1 expression was found in nuclear and cytoplasmic cell fractions of RR. After irradiation PD-L1 decreased in nuclear fractions and increased in cytoplasmic fractions of RR cells. In contrast, RS cell lines did not express PD-L1, neither in the nucleus nor in cytoplasmic fractions. Additionally, overexpression of PD-L1 in RS cells led to a proportional increase of vital PD-L1 positive cells after irradiation. Moreover, co-immunoprecipitation experiments revealed an interaction between Akt-1 and PD-L1, mostly in irradiated RR cells compared to RS cells suggesting a differential influence of PD-L1 on cell signaling. In summary, our data imply the need for different therapeutic strategies dependent on the molecular context in which PD-L1 is embedded.
Photodetachment study of the1s3s4s4Sresonance in He− (1997)

A Feshbach resonance associated with the ${1s3s4s}^{4}S$ state of He${}^{\ensuremath{-}}$ has been observed in the He${(1s2s}^{3}S)$ + ${e}^{\ensuremath{-}}(\ensuremath{\epsilon}s)$ partial photodetachment cross section. The residual He${(1s2s}^{3}S)$ atoms were resonantly ionized and the resulting He${}^{+}$ ions were detected in the presence of a small background. A collinear laser-ion beam apparatus was used to attain both high resolution and sensitivity. We measured a resonance energy ${E}_{\mathrm{r}}=2.959255(7)$ eV and a width $\ensuremath{\Gamma}=0.19(3)$ meV, in agreement with a recent calculation.
High-peak power Yb-doped fiber laser system in 68-&#x00B5;m core multimode fiber with second air-hole cladding structure. (2009)

We have developed a high-peak and high-average power Yb-doped fiber laser system with second air-hole cladding structure. The near-field pattern of the output beam is near single mode (LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> ) due to a bend in part of multi-mode fiber. Advantages of MMF double-clad fiber with second air hole cladding over the conventional double cladding fiber using a polymer cladding are a high numerical aperture (NA), suppression of skew rays and reduction of heat deposition. The laser output power of 300 W and slope efficiency of 74% was achieved in the cw laser oscillation with air-hole double cladding fiber.
Oil and water? High performance garbage collection in Java with MMTk (2004)

Increasingly popular languages such as Java and C# require efficient garbage collection. This paper presents the design, implementation, and evaluation of MMTk, a Memory Management Toolkit for and in Java. MMTk is an efficient, composable, extensible, and portable framework for building garbage collectors. MMTk uses design patterns and compiler cooperation to combine modularity and efficiency. The resulting system is more robust, easier to maintain, and has fewer defects than monolithic collectors. Experimental comparisons with monolithic Java and C implementations reveal MMTk has significant performance advantages as well. Performance critical system software typically uses monolithic C at the expense of flexibility. Our results refute common wisdom that only this approach attains efficiency, and suggest that performance critical software can embrace modular design and high-level languages.