bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints
Authors: Awale Mahendra , Jin Xian , Reymond Jean-Louis 
Published: February 2015

Abstract

Background
Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures).

Results
Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances.

Conclusions
3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects.
Analysis and experimental evaluation of the frequency response of an indoor radiating cable in the UHF band
Authors: Seseña-Osorio Jorge A , Zaldívar-Huerta Ignacio E , Aragón-Zavala Alejandro , Castañón-Ávila Gerardo A 
Published: February 2015

Abstract
We present the modeling of the frequency response of the channel for a radiating cable system by using an autoregressive model for an indoor environment. The coefficients of the autoregressive model are determined from the experimental channel frequency response. Measurements were carried out in an indoor environment, in particular on the second floor of a university building in the frequency range of 1.3 to 1.8 GHz by using a vector network analyzer. It is demonstrated that the use of a second-order model provides a better representation of the behavior of the channel. In this context, the coherence bandwidth and the rms delay spread show dependence with the receiver position along the radiating cable length. This dependence is crucial and must be taken into account in the design and study of broadband systems with mobility because the rms delay spread and coherence bandwidth are used to describe the time dispersion and the frequency selectivity of the multipath fading channels, respectively.
Prognostic significance of tumour stroma ratio in inflammatory breast cancer
Authors: Downey Candice L , Thygesen Helene H , Sharma Nisha , Shaaban Abeer M 
Published: February 2015

Abstract
Tumour stroma ratio (TSR) is emerging as an important prognostic indicator in cancer. We have previously shown TSR to be prognostic in oestrogen receptor positive breast cancer. Its role in inflammatory breast cancer, a rare but aggressive form of breast cancer, has not been identified. Here we aimed to determine the prognostic significance of TSR in a cohort of patients with inflammatory breast carcinoma.
TSR was measured by point counting virtual H&E stained tissue sections in 45 inflammatory breast cancer cases. The whole tumour area was sampled. Optimum cut-offs to distinguish high and low TSR was determined by log-rank test. The relationship of TSR to overall survival and disease-free survival (DFS) was analysed alongside multivariate analysis.
The optimal cut-offs between high and low TSR were determined to be 31% for OS and 46% for DFS. There was no significant difference in OS (p = 0.53) nor DFS (p = 0.66) between high and low TSR groups. Multivariate analysis did not demonstrate any new trends, within the limits of a small data sample. A significant correlation was found between pathological response to neoadjuvant chemotherapy and survival (p = 0.008).
There is no evidence that TSR has prognostic significance in inflammatory breast cancer. When compared with published data in non-inflammatory breast carcinoma, this supports the view that differences in stromal biology exist between tumour types and highlights the importance of considering this when interpreting the prognostic value of TSR. However, these findings must be interpreted in the light of the small sample size.
Helicobacter cinaedi infection in patients with diabetes: a case report
Authors: Ishibashi Ryoichi , Nakamura Susumu , Takemoto Minoru , Mukai Chiaki , Yokote Koutaro 
Published: February 2015

Abstract

Background

Helicobacter cinaedi causes bacteremia without characteristic clinical symptoms and is firstly isolated from human immunodeficiency virus (HIV)-positive homosexual men.

Findings
Here we describe, for the first time case report, two female patients with diabetes who had H. cinaedi bacteremia. Some cases of H. cinaedi bacteremia may require long-term administration of multiple antibiotics prior to the resolution of infection.

Conclusions
Therefore, these cases indicate that it is important to consider H. cinaedi in patients with diabetes presenting with bacteremia, especially in patients with poor glycemic control.
Characterization of the Interaction between Heme and a Parallel G-Quadruplex DNA Formed from d(TTAGGGT)
Authors: Shimizu Haruna , Tai Hulin , Saito Kaori , Shibata Tomokazu , Kinoshita Masashi , Yamamoto Yasuhiko 
Published: February 2015

Abstract
The molecular structure and heme electronic structure of a complex (heme–(d(TTAGGGT))4 complex) between heme and a parallel G-quadruplex DNA formed from heptanucleotide d(TTAGGGT), i.e., (d(TTAGGGT))4, have been characterized using 1H NMR. The study demonstrated that the heme is accommodated between G6 and T7 of the G-quadruplex DNA to form a 1:1 complex between the heme and DNA. The spin state of the heme Fe3+ of the heme(Fe3+)–(d(TTAGGGT))4 complex exhibited a characteristic pH-dependent change from a high spin (HS) state, i.e., S = 5/2, at low pH to a thermal spin equilibrium between the HS and low spin state (LS), i.e., S = 1/2, at high pH, with a midpoint at the pH value of 8.9 ± 0.2. The pH-dependent spin state change of the heme(Fe3+)–(d(TTAGGGT))4 complex was similar to that of metmyoglobin (T. M. McGrath and G. N. La Mar, Biochim. Biophys. Acta, 1978, 534, 99–111), demonstrating that these two systems are highly alike in terms of the heme environment. This finding provides novel insights as to the design of the heme–DNA complexes that exhibit catalytic activities similar to those of hemoproteins.
Google Earth: Inspiration and Instrument for the Study of Ancient Civilizations
Authors: Klokočník Jaroslav , Kostelecký Jan , Pavelka Karel 
Published: February 2015

Satellite imaging is well known as a useful tool in many scientific disciplines and various applications. Google Earth, with its free access, is now - thanks to increasing resolution and precision - such a tool. It can be very inspiring. It improves the visualization and dissemination of scientific data, and opens doors to new discoveries. For example, many Nasca geoglyphs are now visible to Google Earth and so are the orientations of Chinese pyramids, which appear to be laid out with the aid of a magnetic compass. Google Earth also infor-med us about the “new” archaeological locality Atzompa close to the well known “Monte Alban” near Oaxaca (Mexico), which we then visited (in March 2010). Google Earth can also “see” prehistoric causeways in Mesoamerica, “sacbeob” and in the Chaco valley (New Mexico). We find that Google Earth can save time and resources to researches significantly: before, during and after field works and measurements; we present examples.
The Virtual 3D Reconstruction of the East Pediment of the Temple of Zeus at Olympia – Presentation of an Interactive CD-ROM
Authors: Patay-Horváth András 
Published: February 2015

The paper gives an overview of a two-years project concerning a major monument of ancient Greek art and presents the interactive, bilingual (English/Hungarian) CD-ROM, which is intended to summarize and visualize its final results. The presented project approaches a century-old controversy in a new way by producing a virtual 3D reconstruction of a monumental marble group. Digital models of the statues were produced by scanning the original fragments and by reconstructing them virtually. The virtual model of the pediment surrounding the sculptures was prepared on the basis of the latest architectural studies and afterwards the reconstructed models were inserted in this frame, in order to test the technical feasibility and aesthetic effects the four possible arrangements. The resulting models enable easy and very instructive experimentation, which would be otherwise impossible with the originals and/or very expensive and not very practicable with traditional tools (e.g. real-size plaster models). The complete model can effectively be used to verify the results of earlier or more recent reconstructions presented only in simple drawings. In addition, the 3D models of the individual fragments can be used for further research and for visualization. The documentary CD-ROM presenting the full background, the methods and the conclusions of the project contains beside a comprehensive text various kinds of supporting documents (images, 3D models, papers, broadcasts, audiovisual material). It is addressed to a mixed audience: a picture gallery, a short documentary movie some other attachments including a selected bibliography is intended for the general public, but scholarly publications, presentations on related problems are also included for specialists interested in certain details.
Experiences in Photogrammetric and Laser Scanner Surveing of Architectural Heritage
Authors: Caprioli Mauro , Minchilli Maurizio , Scognamiglio Alfredo 
Published: February 2015

The integration of different methodologies and simplification of procedures is surely one of the most important current themes in survey techniques for researching cultural heritage, especially for architectural heritage. The traditional methods for the metric survey of an architectural building (including micro geodesy and the stereophotogrammetric survey) are currently being consolidated. However, in the field of the architectural, artistic and archaeological survey, new technologies are now available and this knowledge needs to be more widely used, especially where the heritage is greater and so maintenance is as necessary as it is onerous. This report proposes some operative considerations, which derive from experience developed using the most modern technologies available, in order to compare and discuss the achievable accuracies (even if they are not always strictly necessary) and the operating modalities, especially for architectural surveys. So, the aim of this report is to verify that the simplification of procedures and cheaper solutions do not bring variations to the necessary metric precision or expert photointerpretation analysis. However, it is clear that, without considering the purposes and objectives of the survey, it would not be correct to appraise the survey methods and to classify those using reliability and accuracy criteria. In fact, the objective of a survey determines which tool will be used, according to the requests of the survey client to the survey expert.
Bacterial Pancarditis with Myocardial Abscess: Successful Surgical Intervention in a 14-Month-Old Boy
Authors: Yoon Jonathan K. , Rahimi M. Babak , Fiore Andrew , Schowengerdt Kenneth , Jureidini Saadeh B. 
Published: February 2015

A 14-month-old boy with a structurally normal heart presented with signs of cardiac tamponade caused by purulent pericarditis. During his hospital stay, mitral and tricuspid valve endocarditis developed, and a ventricular septal abscess expanded despite appropriate, prolonged antibiotic therapy for methicillin-resistant Staphylococcus aureus. The day before scheduled surgical correction, the abscess ruptured, creating a septal aneurysm. Surgical intervention resulted in an excellent outcome. Throughout the patient's 67-day hospitalization, the use of echocardiography was crucial in monitoring and diagnosis.
In addition to reporting this case, we discuss our diagnostic and treatment considerations. To our knowledge, this is only the 4th report of S. aureus bacterial pancarditis with myocardial abscess.
Incidental Left Atrial Blood Cyst in a Patient Undergoing Transcatheter Aortic Valve Replacement
Authors: Suero Gregory , Shah Moneal , Hughes-Doichev Rachel 
Published: February 2015

Blood cysts of the heart are benign cardiovascular tumors found incidentally in approximately 50% of infants who undergo autopsy at less than 2 months of age. These congenital cysts, frequently present on the atrioventricular valves of infants, are exceedingly rare in adults. Nonetheless, in adults, cardiac blood cysts have been found on the mitral valve, papillary muscles, right atrium, right ventricle, left ventricle, and aortic, pulmonic, and tricuspid valves. Reported complications include left ventricular outflow obstruction, occlusion of the coronary arteries, valvular stenosis or regurgitation, and embolic stroke.
In high-risk patients with severe aortic stenosis, transcatheter aortic valve replacement has emerged as an alternative to surgical replacement. Transesophageal echocardiography plays a fundamental role in evaluating the feasibility of intraprocedural transcatheter aortic valve replacement, in measuring aortic annular size, in guiding placement of the prosthetic device, and in looking for possible complications. The embolic risk of rapid pacing and transcatheter aortic valve replacement in a patient with an intracardiac blood cyst is unknown, and such a case has not, to our knowledge, been reported heretofore. We present the case of a 78-year-old woman with severe aortic stenosis, in whom a blood cyst was incidentally found in the left atrium upon transesophageal echocardiography. She underwent successful transcatheter aortic valve replacement without embolic complication.
Early Detection of a Cavopulmonary Tumor Embolus with the Use of Transesophageal Echocardiography
Authors: El-Sayed Ahmed Magdy M. , Al-Najjar Raed M. , Aftab Muhammad , Anton James M. , Colen John S. , Reul Ross M. 
Published: February 2015

Pulmonary tumor embolization from renal cell carcinoma is associated with severe cardiopulmonary morbidity and high perioperative mortality rates. We report the case of a 71-year-old woman who presented with right-sided abdominal pain. Magnetic resonance images revealed a mass originating from the upper pole of the right kidney and extending into the infrahepatic portion of the inferior vena cava. Transesophageal echocardiography was continuously used to monitor the mass during intended radical nephrectomy and tumor resection. When the right kidney was mobilized, intracaval thrombus detached and migrated to the patient's right atrium, causing severe hemodynamic instability. After emergent sternotomy and during the initiation of cardiopulmonary bypass, the mass was no longer echocardiographically detectable in the heart; it was soon removed completely from the left pulmonary artery. The mass was a renal cell carcinoma.
We recommend the use of transesophageal echocardiography as an efficient diagnostic tool in the early detection of pulmonary tumor embolization during the resection of renal cell carcinoma that involves the inferior vena cava.
Echocardiographic versus Histologic Findings in Marfan Syndrome
Authors: Gu Xiaoyan , He Yihua , Li Zhian , Han Jiancheng , Chen Jian , Nixon J.V. (Ian) 
Published: February 2015

This retrospective study attempted to establish the prevalence of multiple-valve involvement in Marfan syndrome and to compare echocardiographic with histopathologic findings in Marfan patients undergoing valvular or aortic surgery.
We reviewed echocardiograms of 73 Marfan patients who underwent cardiovascular surgery from January 2004 through October 2009. Tissue histology was available for comparison in 29 patients.
Among the 73 patients, 66 underwent aortic valve replacement or the Bentall procedure. Histologic findings were available in 29 patients, all of whom had myxomatous degeneration. Of 63 patients with moderate or severe aortic regurgitation as determined by echocardiography, 4 had thickened aortic valves. The echocardiographic findings in 18 patients with mitral involvement included mitral prolapse in 15. Of 11 patients with moderate or severe mitral regurgitation as determined by echocardiography, 4 underwent mitral valve repair and 7 mitral valve replacement. Histologic findings among mitral valve replacement patients showed thickened valve tissue and myxomatous degeneration. Tricuspid involvement was seen echocardiographically in 8 patients, all of whom had tricuspid prolapse. Two patients had severe tricuspid regurgitation, and both underwent repair. Both mitral and tricuspid involvement were seen echocardiographically in 7 patients.
Among the 73 patients undergoing cardiac surgery for Marfan syndrome, 66 had moderate or severe aortic regurgitation, although their valves manifested few histologic changes. Eighteen patients had mitral involvement (moderate or severe mitral regurgitation, prolapse, or both), and 8 had tricuspid involvement. Mitral valves were most frequently found to have histologic changes, but the tricuspid valve was invariably involved.
Acute Surgical Pulmonary Embolectomy: A 9-Year Retrospective Analysis
Authors: Hartman Alan R. , Manetta Frank , Lessen Ronald , Pekmezaris Renee , Kozikowski Andrzej , Jahn Lynda , Akerman Meredith , Lesser Martin L. , Glassman Lawrence R. , Graver Michael , Scheinerman Jacob S. , Kalimi Robert , Palazzo Robert , Vatsia Sheel , Pogo Gustave , Hall Michael , Yu Pey-Jen , Singh Vijay 
Published: February 2015

Acute pulmonary embolism is a substantial cause of morbidity and death. Although the American College of Chest Physicians Evidence-Based Clinical Practice Guidelines recommend surgical pulmonary embolectomy in patients with acute pulmonary embolism associated with hypotension, there are few reports of 30-day mortality rates.
We performed a retrospective review of acute pulmonary embolectomy procedures performed in 96 consecutive patients who had severe, globally hypokinetic right ventricular dysfunction as determined by transthoracic echocardiography. Data on patients who were treated from January 2003 through December 2011 were derived from health system databases of the New York State Cardiac Surgery Reporting System and the Society of Thoracic Surgeons. The data represent procedures performed at 3 tertiary care facilities within a large health system operating in the New York City metropolitan area.
The overall 30-day mortality rate was 4.2%. Most patients (68 [73.9%]) were discharged home or to rehabilitation facilities (23 [25%]). Hemodynamically stable patients with severe, globally hypokinetic right ventricular dysfunction had a 30-day mortality rate of 1.4%, with a postoperative mean length of stay of 9.1 days. Comparable findings for hemodynamically unstable patients were 12.5% and 13.4 days, respectively.
Acute pulmonary embolectomy can be a viable procedure for patients with severe, globally hypokinetic right ventricular dysfunction, with or without hemodynamic compromise; however, caution is warranted. Our outcomes might be dependent upon institutional capability, experience, surgical ability, and careful patient selection.
Meta-Analysis of CHADS2 versus CHA2DS2-VASc for Predicting Stroke and Thromboembolism in Atrial Fibrillation Patients Independent of Anticoagulation
Authors: Zhu Wen-Gen , Xiong Qin-Mei , Hong Kui 
Published: February 2015

Two validated scoring systems for predicting embolic risk, CHADS2 and CHA2DS2-VASc, contribute to optimizing antithrombotic prescription practices in patients who have atrial fibrillation. However, data about anticoagulated patients are sparse. We compared CHADS2 and CHA2DS2-VASc, in terms of their predictive risk evaluation, in patients with atrial fibrillation who were and were not taking anticoagulants.
We systematically searched the Cochrane Library, PubMed, and Embase databases for studies of the comparative diagnostic performance of CHADS2 and CHA2DS2-VASc. We identified 12 cohort studies for meta-analysis. With regard to the occurrence of cardiovascular events individually, patients with CHA2DS2-VASc scores ≥2 have a greater risk of stroke (risk ratio [RR]=5.15; 95% confidence interval [CI], 3.85–6.88; P <0.00001) and thromboembolism (RR=5.96; 95% CI, 5.50–6.45; P <0.00001) (Pdiff=0.34) than do patients with CHA2DS2-VASc scores <2, independent of anticoagulation therapy (RR=5.76; 95% CI, 5.23–6.35; P <0.00001 in anticoagulated patients; and RR=6.12; 95% CI, 5.40–6.93; P <0.00001 in patients not taking anticoagulants; Pdiff=0.45). The pooled RR estimates indicate an approximate 6-fold increase in the risk of endpoint events in patients with CHA2DS2-VASc scores ≥2 (RR=5.90; 95% CI, 5.46–6.37; P <0.0001).
These results clearly indicate the discriminative capacity of the CHA2DS2-VASc score for stroke, thromboembolic events, or both, independent of optimal anticoagulation. The CHA2DS2-VASc score enables the identification of patients who are at genuinely high risk and can direct the selection of appropriate therapeutic approaches.
Thiol-based redox switches in prokaryotes
Authors: Hillion Melanie , Antelmann Haike 
Published: February 2015

AbstractBacteria encounter reactive oxygen species (ROS) as a consequence of the aerobic life or as an oxidative burst of activated neutrophils during infections. In addition, bacteria are exposed to other redox-active compounds, including hypochloric acid (HOCl) and reactive electrophilic species (RES) such as quinones and aldehydes. These reactive species often target the thiol groups of cysteines in proteins and lead to thiol-disulfide switches in redox-sensing regulators to activate specific detoxification pathways and to restore the redox balance. Here, we review bacterial thiol-based redox sensors that specifically sense ROS, RES and HOCl via thiol-based mechanisms and regulate gene transcription in Gram-positive model bacteria and in human pathogens, such asStaphylococcus aureusandMycobacterium tuberculosis. We also pay particular attention to emerging widely conserved HOCl-specific redox regulators that have been recently characterized inEscherichia coli. Different mechanisms are used to sense and respond to ROS, RES and HOCl by 1-Cys-type and 2-Cys-type thiol-based redox sensors that include versatile thiol-disulfide switches (OxyR, OhrR, HypR, YodB, NemR, RclR, Spx, RsrA/RshA) or alternative Cys phosphorylations (SarZ, MgrA, SarA), thiol-S-alkylation (QsrR), His-oxidation (PerR) and methionine oxidation (HypT). In pathogenic bacteria, these redox-sensing regulators are often important virulence regulators and required for adapation to the host immune defense.