gebhart/patrepeval huggingface dataset:
The Capsule Polymerase CslB of Neisseria meningitidis Serogroup L Catalyzes the Synthesis of a Complex Trimeric Repeating Unit Comprising Glycosidic and Phosphodiester Linkages (2015)

Neisseria meningitidis is a human pathogen causing bacterial meningitis and sepsis. The capsular polysaccharide surrounding N. meningitidis is a major virulence factor. The capsular polysaccharide consists of polyhexosamine phosphates in N. meningitidis serogroups A and X. The capsule polymerases (CPs) of these serogroups are members of the Stealth protein family comprising d-hexose-1-phosphate transferases from bacterial and protozoan pathogens. CslA, one of two putative CPs of the pathophysiologically less relevant N. meningitidis serogroup L, is one of the smallest known Stealth proteins and caught our attention for structure-function analyses. Because the N. meningitidis serogroup L capsule polymer consists of a trimeric repeating unit ([→3)-β-d-GlcNAc-(1→3)-β-d-GlcNAc-(1→3)-α-d-GlcNAc-(1→OPO3→]n), we speculated that the two predicted CPs (CslA and CslB) work together in polymer production. Consequently, both enzymes were cloned, overexpressed, and purified as recombinant proteins. Contrary to our expectation, enzymatic testing identified CslB to be sufficient to catalyze the synthesis of the complex trimeric N. meningitidis serogroup L capsule polymer repeating unit. No polymerase activity was detected for CslA, although the enzyme facilitated the hydrolysis of UDP-GlcNAc. Bioinformatics analyses identified two glycosyltransferase (GT) domains in CslB. The N-terminal domain modeled with 100% confidence onto a number of GT-A folded proteins, whereas the C-terminal domain modeled with 100% confidence onto TagF, a GT-B folded teichoic acid polymerase from Staphylococcus epidermidis. Amino acid positions known to have critical catalytic functions in the template proteins were conserved in CslB, and their point mutation abolished enzyme activity. CslB represents an enzyme of so far unique complexity regarding both the catalyzed reaction and enzyme architecture.
Vertical relative displacements in a medium-rise CLT-building (2010)

Several buildings have been built using clt-panels (cross-laminated timber) in Sweden and Europe during the last few years. There are various advantages of using clt in the load-bearing system instead of using the conventional stud and rail technique. One of the major advantages is that the technique enables larger freedom for the architect since the capacity of the panels for vertical as well as for horizontal loads is much higher as compared to conventional timber building technique using studs and rails. This implies that the design of the structure is not to the same extent as before limited due to the chosen material of load bearing system but enables the usage of wood in more complex structures that were not likely to be built with wood before.
Structural Insights into Protein-Protein Interactions Involved in Bacterial Cell Wall Biogenesis (2016)

The bacterial cell wall is essential for survival, and proteins that participate in its biosynthesis have been the targets of antibiotic development efforts for decades. The biosynthesis of its main component, the peptidoglycan, involves the coordinated action of proteins that are involved in multi-member complexes which are essential for cell division (the "divisome") and/or cell wall elongation (the "elongasome"), in the case of rod-shaped cells. Our knowledge regarding these interactions has greatly benefitted from the visualization of different aspects of the bacterial cell wall and its cytoskeleton by cryoelectron microscopy and tomography, as well as genetic and biochemical screens that have complemented information from high resolution crystal structures of protein complexes involved in divisome or elongasome formation. This review summarizes structural and functional aspects of protein complexes involved in the cytoplasmic and membrane-related steps of peptidoglycan biosynthesis, with a particular focus on protein-protein interactions whereby disruption could lead to the development of novel antibacterial strategies.
6.2 /spl Anstrom/ In/sub 0.2/Al/sub 0.8/Sb/InAs/sub 0.7/Sb/sub 0.3/ HEMTs for low -voltage high-frequency applications (2004)

The paper presents the performance of In/sub 0.2/Al/sub 0.8/Sb/InAs/sub 0.7/Sb/sub 0.3/ HEMTs that are fabricated for the first time in a uniform alloy of InAs/sub 0.7/Sb/sub 0.3/ as the channel layer with adjacent In/sub 0.2/Al/sub 0.8/Sb barrier layers, with a lattice constant of 6.2/spl Aring/. The paper also presents the cross-sectional view of the material structure used in the fabrication process, X-ray analysis spectrum of the material structure, diffraction peaks of the layers, drain characteristics of HEMT and gate transfer characteristics as a function of gate bias. The addition of Sb to the InAs channel offers the possibility of improvement in low-voltage high-frequency applications.
Reaction of active methylene compounds with carbon disulfide in the presence of ammonia. III. Reaction of cyclopentanone and cycloheptanone (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of active methylene compounds with carbon disulfide in the presence of ammonia. III. Reaction of cyclopentanone and cycloheptanoneTatsuo Takeshima, Masataka Yokoyama, Tsuneo Imamoto, Makiko Akano, and Hiroe AsabaCite this: J. Org. Chem. 1969, 34, 3, 730–732Publication Date (Print):March 1, 1969Publication History Published online1 May 2002Published inissue 1 March 1969https://pubs.acs.org/doi/10.1021/jo01255a054https://doi.org/10.1021/jo01255a054research-articleACS PublicationsRequest reuse permissionsArticle Views285Altmetric-Citations62LEARN 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
Data from Response to Neoadjuvant Targeted Therapy in Operable Head and Neck Cancer Confers Survival Benefit (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Neoadjuvant targeted therapy provides a brief, preoperative window of opportunity that can be exploited to individualize cancer care based on treatment response. We investigated whether response to neoadjuvant therapy during the preoperative window confers survival benefit in patients with operable head and neck squamous cell carcinoma (HNSCC).&lt;/p&gt;Patients and Methods:&lt;p&gt;A pooled analysis of treatment-naïve patients with operable HNSCC enrolled in one of three clinical trials from 2009 to 2020 (NCT00779389, NCT01218048, NCT02473731). Neoadjuvant regimens consisted of EGFR inhibitors (&lt;i&gt;n&lt;/i&gt; = 83) or anti-ErbB3 antibody therapy (&lt;i&gt;n&lt;/i&gt; = 9) within 28 days of surgery. Clinical to pathologic stage migration was compared with disease-free survival (DFS) and overall survival (OS) while adjusting for confounding factors using multivariable Cox regression. Circulating tumor markers validated in other solid tumor models were analyzed.&lt;/p&gt;Results:&lt;p&gt;92 of 118 patients were analyzed; all patients underwent surgery following neoadjuvant therapy. Clinical to pathologic downstaging was more frequent in patients undergoing neoadjuvant targeted therapy compared with control cohort (&lt;i&gt;P&lt;/i&gt; = 0.048). Patients with pathologic downstage migration had the highest OS [89.5%; 95% confidence interval (CI), 75.7–100] compared with those with no stage change (58%; 95% CI, 46.2–69.8) or upstage (40%; 95% CI, 9.6–70.4; &lt;i&gt;P&lt;/i&gt; = 0.003). Downstage migration remained a positive prognostic factor for OS (HR, 0.22; 95% CI, 0.05–0.90) while adjusting for measured confounders. Downstage migration correlated with decreased circulating tumor markers, &lt;i&gt;SOX17&lt;/i&gt; and &lt;i&gt;TAC1&lt;/i&gt; (&lt;i&gt;P&lt;/i&gt; = 0.0078).&lt;/p&gt;Conclusions:&lt;p&gt;Brief neoadjuvant therapy achieved pathologic downstaging in a subset of patients and was associated with significantly better DFS and OS as well as decreased circulating methylated &lt;i&gt;SOX17&lt;/i&gt; and &lt;i&gt;TAC1&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Structure-Based Screening Reveals a Ligand That Stabilizes the [2Fe-2S] Clusters of Human mitoNEET and Reduces Ovarian Cancer Cell Proliferation (2022)

Human NEET proteins play an important role in a variety of diseases, including cancer. Using the recently published X-ray structure of the human mNT-M1 complex, we screened a commercial chemical compound library and identified a new human mitoNEET (mNT) binding ligand (NTS-01). Biochemical investigations revealed that NTS-01 specifically binds to the human mNT protein and stabilizes its [2Fe-2S] clusters under oxidative conditions <i>in vitro</i>. Treatment of ovarian cancer cells with NTS-01 induces ovarian cancer (SKOV-3) mitochondrial fragmentation (fission) and reduces ovarian cancer cell proliferation in a 2D single-layer cell culture, as well as in a 3D-spheroids culture. The NTS-01 molecule represents therefore a new lead compound for further drug design studies attempting to develop efficient treatment against ovarian cancer.
Development of Multistage Magnetic Deposition Microscopy (2008)

Magnetic deposition microscropy (MDM) combines magnetic deposition and optical analysis of magnetically tagged cells into a single platform. Our multistage MDM uses enclosed microfabricated channels and a magnet assembly comprising four zones in series. The enclosed channels alleviate the problem plaguing previous versions of MDM: scouring of the cell deposition layer by the air-liquid interface as the channel is drained. The four-zone magnet assembly was designed to maximize capture efficiency, and experiments yielded total capture efficiencies of >99% of fluorescent- and magnetically-labeled Jurkat cells at reasonable throughputs (10(3) cells/min). A digital image processing protocol was developed to measure the average pixel intensities of the deposited cells in different zones, indicative of the marker expression. Preliminary findings indicate that the multistage MDM may be suitable for depositing cells and particles in successive zones according to their magnetic properties (e.g., magnetic susceptibilities or magnetophoretic mobilities). The overall goal is to allow the screening of multiple disease conditions in a single platform.
A 1.0-Mb/s 198-pJ/bit Bluetooth Low-Energy Compatible Single Sideband Backscatter Uplink for the NeuroDisc Brain–Computer Interface (2019)

Wireless brain-computer interfaces (BCIs) are highly energy constrained because of the need to minimize battery size and weight, as well as the need to minimize the thermal dissipation into the living tissue. We demonstrate an ultralow-power Bluetooth Low Energy (BLE) v5.0 compatible backscatter communication uplink for the NeuroDisc BCI. This backscatter approach is compatible with completely unmodified BLE devices such as PCs, smartphones, and tablets and has an energy consumption of under 200 pJ/bit, over 50× less than commercially available BLE transmitters. This article is the first to present an analysis and demonstration of single sideband (SSB) BLE backscatter, which increases the available channel power by +3 dB while suppressing out-of-channel emissions. An analytic model of SSB backscatter communication is provided, along with simulations showing how nonidealities in the achieved backscatter constellation impact opposite-sideband suppression. The experimental measurements of in-channel gain and opposite-sideband suppression are provided. Additional experiments demonstrate a range of 6 m using a +20-dBm external carrier source and an unmodified Nordic Semiconductor nRF51DK BLE adapter, while uplinking prerecorded neural data sampled at 500 Hz.
Ga68-NOTA-CHSg and Tc99m-CHSg Labeled Microspheres for Lung Perfusion and Liver Radiomicrospheres Therapy Planning (2013)

Fast biodegradable (12 h < half-life < 48 h) radioactive labeled microspheres are needed for PET and SPECT lung perfusion and radiomicrosphere therapy planning. An emulsion method was used to create 30.1 ±4.8 μ m size range microspheres with biodegradable Chitosan glycol (CHSg). Microspheres were characterized and labeled with (99m)Tc or (68)Ga as an alternative to MAA in perfusion PET and SPECT studies. Surface decoration of CHSg microspheres with p-SCN-Bn-NOTA was performed to increase (68)Ga in vivo stability. (99m)Tc was labeled directly to the CHSg microspheres. Labeling yield and in vitro radiochemical stability were evaluated. In vitro CHSg microsphere degradation half-life was ~24 hours in porcine blood. Labeled microspheres were injected into Sprague Dawley rats and biodistribution was determined after 2 and 4 hours. Both (99m)Tc-CHSg and (68)Ga-NOTA-CHSg were quickly allocated in the lungs after injection. (99m)Tc-CHSg showed 91.6 ± 6.5% and 83.2 ± 4.1% of the decay corrected injected activity remaining in the lungs after 2 and 4 hours, respectively. For the obtained (68)Ga-NOTA-CHSg microspheres, lung allocation was very high with 98.9 ± 0.2% and 95.6 ± 0.9% after 2 and 4 hours, respectively. The addition of p-SCN-Bn-NOTA acts as a radioprotectant eliminating the released (68)Ga activity from the lungs to the bladder protecting the other organs.
A set of highly water-soluble tetraethyleneglycol-substituted Zn(ii) phthalocyanines: synthesis, photochemical and photophysical properties, interaction with plasma proteins and in vitro phototoxicity (2010)

Three Zn(II) phthalocyanines substituted by hydroxyl-terminated tetraethylene glycol chains have been synthesized. In order to evaluate the potential of these highly water-soluble phthalocyanines as type II-photosensitisers for photodynamic therapy, their structure-activity relationship was assessed by determining relevant photophysical and photochemical properties, such as their aggregation behaviour in aqueous buffers, their fluorescence properties and their efficiency with regard to the generation of singlet oxygen. In addition, evidence for a negligible interaction with plasma proteins in undiluted human plasma was obtained using a recently developed bioanalytical method and compared with the fluorescence quenching approach. These results combined with in vitro data regarding the phototoxicity of these phthalocyanines against HT-29 cancer cells provide evidence for the relevance of the non-peripherally substituted derivative for further in vivo investigations.
Basics and techniques (2004)

This is a comprehensive four-part handbook that covers all aspects of non-destructive evaluation with charged-particles, photons, and neutrons. It provides students, engineers, industrial physicists, and experts in the field with an inclusive source of streamlined information, references, and helpful suggestions.
Neutrophil to lymphocyte ratio predicts intracranial hemorrhage after endovascular thrombectomy in acute ischemic stroke (2018)

NLR is an independent predictor for the development of ICH after EVT. Further studies are needed to investigate the role of the immune system in hemorrhagic complications following EVT, and confirm the value of NLR as a potential biomarker.
Health effects of nanomaterials: A critical appraisal approach and research to practice (2008)

Abstract Background Researchers across the globe are studying health effects of various nanomaterials and nanostructures. Most of these studies are qualitative in nature and lack parallel research to compare and validate the reliability of the findings. Objective This research targets a critical appraisal of such clinical studies by first developing a suitable tool and then evaluating the quality of reporting of these trials. Methods The published articles were collected from a search of electronic databases and bibliographies of identified articles. A critical appraisal (ExpAI) suitable for assessment of such experimental studies was developed and the articles were appraised using this instrument. The main findings of the study were evaluated for their use in the development of new techniques for practice using a linguistic scale. Results Twenty‐eight articles were found to satisfy the inclusion criteria adopted in this research. The methodological qualities of the published studies ranged from marginal to average. Conclusions Though the studies evaluated in this research have proven that nanoparticles do have adverse health effects, nanoparticles should not be discounted without exploring the possibility of using them to benefit companies and the general population. Reengineering should be considered while creating these new systems to overcome the health effects found by various studies. © 2008 Wiley Periodicals, Inc.
Environmental contamination with rhinovirus and transfer to fingers of healthy individuals by daily life activity (2007)

Rhinovirus infection may be acquired by inoculation of virus on fingertips to conjunctiva or nose (self-inoculation). The virus contaminating the fingertips may come from hand contact with someone with a cold or from virus in mucus on environmental surfaces. This study was designed to assess rhinovirus contamination of surfaces by adults with colds and rhinovirus transfer from surfaces to fingertips during normal daily activities. Fifteen adults with natural rhinovirus colds stayed overnight in a local hotel. Ten touched sites in each room were tested for rhinovirus RNA using RT-PCR. Transfer to fingertips of five subjects was examined by drying 10 microl of virus-containing mucus from each subject onto light switches, telephone dial buttons and telephone handsets. After an interval of 1 or 18 hr the subject flipped the light switch, pressed the button, held the handset. Fingertip rinses were tested for virus. Thirty five percent of the 150 environmental sites in the rooms were contaminated. Common virus-positive sites were door handles, pens, light switches, TV remote controls, faucets, and telephones. Rhinovirus was transferred from surfaces to fingertips in 18/30 (60%) trials 1 hr after contamination and in 10/30 (33%) of trials 18 hr (overnight) after contamination. Adults with colds commonly contaminate environmental surfaces with rhinovirus; virus on surfaces can be transferred to a fingertip during normal daily activities.
The E3 Ligase TRAF6 directs FOXP3 localization and facilitates Treg function through K63‐type ubiquitination (2019)

For the immune system to function properly, the activation of leukocytes must be tightly regulated. Failures of immune control mechanisms underlie the aberrant targeting of self‐antigens (i.e. autoimmunity) and the collateral damage of healthy tissues during excessive responses to infectious threats or the unnecessary immune mobilization against innocuous commensal microbes. Foxp3‐expressing CD4+ Regulatory T cells (Tregs) are a major cellular force working to prevent these pathologies of immune dysregulation. These cells characteristically exhibit multiple suppressive function that is absolutely required for the maintenance of immune homeostasis. However, these cells can hamper desirable anti‐tumor immune responses in cancer patients. Accordingly, a relative abundance of Tregs in the tumor microenvironment (TME) is a negative prognostic factor in many cancers. Treg‐depleting or antagonizing strategies show promise as potential interventions capable of unleashing anti‐tumor immunity from suppression. The characteristic gene expression and suppressive function of Tregs depend considerably on the stable expression and activity of the transcription factor FOXP3. While transcriptional regulation of the Foxp3 gene has been studied in depth, both the expression and function of this factor are also modulated at the protein level. However, the molecular players involved in posttranslational FOXP3 regulation are just beginning to be elucidated. We have found that in the absence of the E3 ligase TRAF6 Tregs were dysfunctional in vivo . In these studies, mice with Treg‐restricted deletion of TRAF6 were highly resistant to implanted tumors and displayed enhanced anti‐tumor immunity. We further determined that FOXP3 undergoes lysine‐63 linked (K63) ubiquitination at lysine 262, and this posttranslational modification was mediated by TRAF6. When deprived of TRAF6 activity or rendered insensitive to K63 ubiquitination, FOXP3 displayed aberrant, perinuclear accumulation and disrupted regulatory function. Thus, K63 ubiquitination by TRAF6 ensures proper localization of FOXP3 and facilitates the transcription factor's gene‐regulating activity in Tregs. These results implicate TRAF6 as a key, hitherto unappreciated posttranslational facilitator of FOXP3 stabilization and Treg suppressive function that may be targeted by novel tolerance‐breaking immunotherapies to improve anti‐tumor immunity and combat disease progression in cancer patients. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering (2015)

Tal.Galili@math.tau.ac.il.
The Biology of Colicin M and Its Orthologs (2021)

The misuse of antibiotics during the last decades led to the emergence of multidrug resistant pathogenic bacteria. This phenomenon constitutes a major public health issue. Consequently, the discovery of new antibacterials in the short term is crucial. Colicins, due to their antibacterial properties, thus constitute good candidates. These toxin proteins, produced by E. coli to kill enteric relative competitors, exhibit cytotoxicity through ionophoric activity or essential macromolecule degradation. Among the 25-colicin types known to date, colicin M (ColM) is the only one colicin interfering with peptidoglycan biosynthesis. Accordingly, ColM develops its lethal activity in E. coli periplasm by hydrolyzing the last peptidoglycan precursor, lipid II, into two dead-end products, thereby leading to cell lysis. Since the discovery of its unusual mode of action, several ColM orthologs have also been identified based on sequence alignments; all of the characterized ColM-like proteins display the same enzymatic activity of lipid II degradation and narrow antibacterial spectra. This publication aims at being an exhaustive review about what is currently known on this new family of antibacterial enzymes as well as on their potential use of food preservatives or therapeutic agents.
Synthesis of a key fluorogenic amide, L-arginine-4-methylcoumaryl-7-amide (L-Arg-MCA) and its derivatives. Fluorescence assays for trypsin and papain. (1977)

L-Arginine-4-methylcoumaryl-7-amide 2 and its derivatives, which contain 7-amino-4-methylcoumarin 1 as a key fluorescence amine, were synthesized. The L-antipodes of Nα-benzoyl and Nα-carbobenzoxy derivatives were shown to be the useful fluorogenic substrates for the sensitive determinations of trypsin and papain.