bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to Express Tumor Markers in Bronchoalveolar Lavage
Authors: Caro Gómez de Terreros F.J. , Álvarez-Sala R. , Prados M.C. , Callol L. , Gómez de Terreros Sínchez F.J. , Villamor J. 
Published: January 2018

Introduction Bronchoalveolar lavage (BAL) is a fundamental technique in the diagnosis of different respiratory diseases including lung cancer. Tumor marker values can be determined in the BAL fluid, but controversy still exists about how to express the results. Objective The aim of this study was to determine the best method of expressing tumor markers in BAL, either referring to total proteins or volume of fluid recovered. Patients and Methods A prospective, randomized, non-blind study was carried out. Seventy-six patients (72 men and 4 women) diagnosed with lung cancer and 17 subjects without respiratory disease were included. BAL was performed in all patients and the fluid retrieved was divided into two fractions: a bronchiolar fraction (F0) and an alveolar fraction (F1). Five tumor markers: cytokeratin fragment 19 (CYFRA 21–1), squamous cell carcinoma antigen (SCC), tissue polypeptide antigen (TPA), tissue polypeptide-specific antigen (TPS) and neuron-specific enolase (NSE) as well as total protein were measured in both fractions. The concentrations were expressed in relation to the volume of BAL fluid recovered (ng or mU/mL) and in milligrams of total protein of lavage fluid (ng or mU/mg TP). The SPSS 11.01 software was used for statistical analysis. Mann-Whitney U test and ROC curves were developed when significant differences were found. Results We found significant differences in the CYFRA 21-1 values in the two BAL fractions and in both ways of expressing its concentration; in SCC in F1 expressed in ng/mg TP; in TPA in F0 expressed in mU/mg TP; in TPS in both fractions expressed in mU/mg TP, and in NSE in both fractions in ng/mg TP. The markers that best differentiated tumors from controls (ROC curves) were CYFRA 21-1 in F0 and NSE in both fractions in ng/mg TP. Conclusions Our study demonstrates that the concentrations of tumor markers in BAL expressed in relation to total protein were more effective than if expressed in mL of BAL fluid collected.
Analysis of T-Cell Clonality Pattern in Tumor Samples of Breast Cancer Patients
Authors: Cikota B.M. , Branković-Magić M.V. , Jović V.S. , Radulović S.S. , Magić Z.M. 
Published: January 2018

Purpose and methods A large body of experimental evidence has confirmed that different tumors, including breast carcinomas, can stimulate specific T-cell-mediated immune responses. In this study we have analyzed patterns of T-cell clonality in tumor samples of 54 breast cancer patients classified as lymph node negative, N0 (n=16), or lymph node positive, N+ (n=38). The clonality of T-cells was analyzed by the PCR-PAGE method. Results Monoclonal/oligoclonal (M/O) T-cell populations were found in 15 breast cancer patients, nine N+ and six N0. In all analyzed groups (N+ + N0, N+, N0) the incidence of relapse was not significantly different between patients with M/O and patients with polyclonal T-cells. Comparison of disease-free interval (DFI) between patients divided according to the presence of TCR? monoclonality/oligoclonality showed a marginally significant difference only in the group of N+ patients within the first 24 months of follow-up. Patients with a M/O T-cell population had a shorter DFI than patients with a polyclonal T-cell population. This difference was not observed when the complete follow-up period was considered in the same group of patients. Furthermore, there was no significant difference in overall survival (OS) between patients with M/O and patients with polyclonal T-cells. Conclusion Our results imply that tumor infiltrating T-cells are usually polyclonal. The pattern of T-cell clonality does not correlate with the incidence of relapse and the duration of DFI and OS in the analyzed groups of breast cancer patients, excluding N+ patients with M/O T-cells who had a shorter DFI in the first 24 months of follow-up. This observation suggests that polyclonal T-cell populations may provide a broader spectrum of T-cell-mediated antitumor response.
Elevation of Serum CA 125 and D-Dimer Levels associated with Rupture of Ovarian Endometrioma
Authors: Uharček P. , Mlynček M. , Ravinger J. 
Published: January 2018

Background Patients with endometriosis rarely have a serum CA 125 concentration >100 IU/mL. A raised plasma level of D-dimer indicates active fibrinolysis, either secondary to clot formation or primarily activated. This condition is seldom diagnosed in patients with endometriosis. Case report A 53-year-old woman was referred to our institution for acute abdominal pain. Laparoscopic surgery revealed a large ovarian cyst with rupture on the left side. Preoperative laboratory tests detected high serum CA 125 and D-dimer levels. Adnexectomy was performed, resulting in a sharp decrease in serum CA 125 and D-dimer concentration. We describe the clinical course of the patient. Conclusion Rupture of a large ovarian endometrioma can lead to a high serum concentration of CA 125, a condition which, in addition to the detected pelvic mass, may mimic a malignant process. The increased D-dimer plasma level indicated that a ruptured endometriotic cyst can induce coagulation reactions.
High Expression of Nuclear Factor of Activated T Cells in Chinese Primary Non-Small Cell Lung Cancer Tissues
Authors: Zhang K. , Li N. , Chen Z. , Shao K. , Zhou F. , Zhang C. , Mu X. , Wan J. , Li B. , Feng X. , Shi S. , Xiong M. , Cao K. , Wang X. , Huang C. , He J. 
Published: January 2018

Purpose Nuclear factor of activated T cells (NFAT) has been reported to be involved in the development of various types of cancer including adenocarcinoma of the breast. This research was the first to investigate NFAT protein expression in primary non-small cell lung cancer (NSCLC) tissues from Chinese patients. Methods NFAT protein expression was determined in 130 surgically resected primary NSCLC and matched normal tissues by immunohistochemical analysis. The association between NFAT expression and clinical categorical variables was further analyzed with the SPSS software. Results We found that NFAT expression was much higher in 85 tumor tissues (65.4%) and lower in 45 tumor tissues (34.6%) compared with the matched normal tissues. Further statistical analysis by the chi-square test showed that high expression of NFAT proteins was significantly associated with tumor differentiation (p=0.045), invasion (p=0.031), histology (p<0.0001), tumor size (p=0.038) and cigarette smoking history (p=0.024). However, there was no correlation between the expression of NFAT proteins and pTNM classification, and no difference in 5-year survival rate between patients with high or low expression of NFAT proteins. Multivariate logistic regression analysis for the correlation between NFAT protein expression levels and various characteristics showed a significant association with histology (p=0.008, OR=0.273). Conclusion Our results revealed that high NFAT expression was present in Chinese NSCLCs and that NFAT expression might be involved in the process of human lung cancer development.
Canonical Notch signaling is dispensable for adult steady-state and stress myelo-erythropoiesis
Authors: Duarte Sara , Woll Petter S. , Buza-Vidas Natalija , Chin Desmond Wai Loon , Boukarabila Hanane , Luís Tiago C. , Stenson Laura , Bouriez-Jones Tiphaine , Ferry Helen , Mead Adam J. , Atkinson Deborah , Jin Shaobo , Clark Sally-Ann , Wu Bishan , Repapi Emmanouela , Gray Nicki , Taylor Stephen , Mutvei Anders P. , Tsoi Yat Long , Nerlov Claus , Lendahl Urban , Jacobsen Sten Eirik W. 
Published: January 2018

Key Points
Canonical Notch signaling is dispensable for steady-state and posttransplantation myelopoiesis, as well as stress erythropoiesis. Key lineage regulators and Notch target genes are expressed independent of canonical Notch signaling in myelo-erythropoiesis.
Correction to: Management and investigation of a Serratia marcescens outbreak in a neonatal unit in Switzerland – the role of hand hygiene and whole genome sequencing
Authors: Zingg Walter , Soulake Isabelle , Baud Damien , Huttner Benedikt , Pfister Riccardo , Renzi Gesuele , Pittet Didier , Schrenzel Jacques , Francois Patrice 
Published: January 2018

Abstract
The original article [1] contained an error whereby an erroneous article ID being displayed at the end of the title; the original article has now been corrected to remove this ID.
An objective measure for the assessment and management of fluid shifts in acute major burns
Authors: Kenworthy Pippa , Phillips Michael , Grisbrook Tiffany L. , Gibson William , Wood Fiona M. , Edgar Dale W. 
Published: January 2018

Abstract

Background
Major burns are life threatening. Fluid resuscitation is required for survival to maintain intravascular volumes and prevent hypovolemic shock. Bioimpedance spectroscopy (BIS) has been recognised as a potential method of monitoring fluid shifts after burn and in other disease states. The aims of this study were to examine the reliability of BIS across different dressing conditions and electrode positions, establish the influence of Acticoat™ on BIS variable measures and determine the validity of whole-body BIS to assess net fluid shift in the presence of moderate to major burns.

Methods
An observational longitudinal cohort study was conducted from December 2014 to February 2016. Patients with over 15% total body surface area (TBSA) burns and injury less than 48 h were enrolled in the study. BIS triplicate measures were collected in an open wound and with an ActicoatTM dressing (at 5 half hour intervals). Standard and alternate electrode placements were utilised for the reliability analysis and standard placement only for determining the validity of BIS in moderate to major burns. The ImpediMde SFB7 was used to collect whole-body and segmental BIS measures. Stata statistical software, release 14 was utilised to analyse all results. Descriptive analyses were performed and were reported using the means and standard deviations (SD).

Results
BIS-repeated measures established BIS raw resistance (R), and predicted volume variables were reliable in any condition (intra-class correlation coefficient (ICC) 0.996–0.999, 95% confidence intervals (CI) 0.996–0.999) without a systematic difference. Acticoat™ dressings significantly influenced all BIS-predicted volumes (p ≤ 0.01) as determined by multilevel mixed effects (MLME) linear regression analysis. Validity of BIS was demonstrated by resistance variables significantly decreasing with increasing net ionic fluid shift and increased TBSA (severity of injury) and calculated fluid volumes increasing with increasing net fluid shift and TBSA. BIS resistance also decreased with time as oedema reduced. For clinical use, a calculator was developed to adjust BIS variables when an Acticoat™ dressing is in situ, thus facilitating BIS variable change estimates in real time, with dressings intact.

Conclusion
BIS may be used clinically to monitor fluid volume change in major acute burns.
Stromal Content Is Correlated With Tissue Site, Contrast Retention, and Survival in Pancreatic Adenocarcinoma
Authors: Torphy Robert J. , Wang Zhen , True-Yasaki Aisha , Volmar Keith E. , Rashid Naim , Yeh Benjamin , Johansen Julia S. , Hollingsworth Michael A. , Yeh Jen Jen , Collisson Eric A. 
Published: January 2018

Purpose Desmoplastic stroma is a cardinal feature of primary pancreatic ductal adenocarcinoma (PDA), but its effects on the biology, prognosis, and therapeutic outcomes in the disease are not known. We developed an automated method to assess tumor stroma density (TSD) and investigated computed tomography (CT) correlates of stroma in PDA. Patients and Methods We collected PDA samples from rapid autopsy and resection series and digitally annotated samples to quantify TSD. A series of patients who had undergone resection also underwent preoperative multiphasic CT imaging. Results Automated and manual assessments of TSD were highly correlated (ρ = 0.65; P < .001). Solid organ metastases had a lower median TSD than primary tumors ( P < .001). Patients whose tumors had high TSD had prolonged recurrence-free survival (hazard ratio [HR] = 0.51; P = .003) and overall survival (HR = 0.57; P = .008). In another independent dataset, patients whose tumors had high TSD had decreased risk for recurrence (HR = 0.03; P = .003) and death (HR = 0.03; P = .003) at time of resection; however, the protective effect of high TSD diminished over time. Patients with a normalized portovenous phase CT tumor enhancement ratio ≥ 0.40 had a longer time to recurrence after resection ( P = .020). Normalized portovenous phase CT tumor enhancement ratio was significantly correlated with TSD ( P = .003). Conclusion Objective quantitative assessment of stroma in PDA revealed several clinically relevant observations. Stroma was less abundant in metastatic PDA, the primary cause of mortality associated with PDA. High stromal content correlated with favorable outcome in patients with resected tumors, implying a protective effect of stroma and suggesting careful consideration of active stromal depletion therapies. Standard, multiphase CT imaging correlated with stroma content and clinical outcome, indicating that noninvasive assessment of stroma is a feasible sensitivity enrichment approach in PDA.
Effects of Electrical Transcutaneous Vagus Nerve Stimulation on the Perceived Intensity of Repetitive Painful Heat Stimuli: A Blinded Placebo- and Sham-Controlled Randomized Crossover Investigation
Authors: Janner Henriette , Klausenitz Catharina , Gürtler Nancy , Hahnenkamp Klaus , Usichenko Taras I. 
Published: January 2018

BACKGROUND:
Transcutaneous vagus nerve stimulation (TVNS) is a promising treatment for acute and chronic pain. However, experimental studies yielded controversial results. We examined if TVNS reduces the perceived intensity of repetitive painful heat stimulation and temporal summation of pain (TSP) in healthy volunteers in comparison with placebo and sham stimulation, as well as no intervention.

METHODS:
In 4 sessions, 90 heat pulse stimuli at individual pain tolerance temperature were applied to the ventral forearm of 49 healthy volunteers (25 women) using a Contact Heat Evoked Potential Stimulator thermode (Medoc, Ramat Yishai, Israel). Pain intensity was assessed with verbal ratings on a numeric pain scale (0–100) at every tenth heat pulse. After the first session in which pain intensities without intervention were evaluated, participants completed 3 sessions in a single-blinded randomized crossover manner: (1) sham stimulation applied at the earlobes, (2) placebo stimulation (inactive device), or (3) TVNS applied at the cymbas conchae. Primary data were analyzed using analysis of variance for repeated measures and t test for paired samples.

RESULTS:
Pain intensity decreased during all interventions as compared to no intervention (ηp
2 = 0.22, P < .001; mean difference TVNS versus no intervention 9.5; 95% confidence interval [CI], 3.6–15.4; P < .001). Hypoalgesic effect of TVNS was better than that of placebo and sham in men before the onset of TSP (mean differences for TVNS versus placebo 6.2; 95% CI, 0.2–12.1; TVNS versus sham 6.2; 95% CI, 0.2–12.1; P < .05). In women, TSP response under TVNS was decreased if compared to no intervention (median difference, 7.5; 95% CI, 3.5–15.0; P = .003).

CONCLUSIONS:
TVNS, placebo, and sham stimulation exerted comparable effects under experimental heat pain stimulation. Only in male participants, TVNS was superior to sham and placebo conditions in the reduction of heat pain before the onset of TSP.
Nucleophilicities of Alcohols and Water in Acetonitrile Based on Reactivities of Benzhydrylium Ions
Authors: Kumara Manikyanahally N , Nakahara Tesshu , Kobayashi Shinjiro , Fujio Mizue , Mishima Masaaki 
Published: January 2018

Abstract
The decay rate constants of benzhydrylium ions generated by laser irradiation in acetonitrile have been determined photometrically. The decay of the stable carbocation with an electron-releasing substituent was decelerated with addition of LiClO4, being attributed to the decrease of the recombination of the cations with the counter anions. On the contrary, the decay of the highly reactive carbocation was accelerated, indicating the occurrence of the reaction with perchlorate anion. The second-order rate constants (k2) for the reactions of benzhydrylium ions with methanol, ethanol, i-propanol, t-butanol, and water were determined in acetonitrile in the presence of 3 mM LiClO4 for benzhydrylium ions less electrophilic than 3,5-dimethyl-4′-chlorobenzhydrylium ion and in the absence of LiClO4 for the remaining reactive benzhydrylium ions. Their logarithms were linearly correlated with the electrophilicity parameters (E) in Mayr’s equation, log k2 = sN(E + N). Based on the correlations the nucleophilicity parameters (N) were evaluated for these nucleophiles in acetonitrile, MeOH, 6.86; EtOH, 7.13; i-PrOH, 6.82; t-BuOH, 5.35; H2O, 5.79. The low nucleophilicity of t-butanol regardless of its high gas-phase basicity representing the inherent nature in molecular structure suggests the importance of steric environment at the transition state of the combination of benzhydrylium ions with nucleophiles.
Synthesis of β-Hydroxy-α,α-disubstituted Amino Acids through the Orthoamide-Type Overman Rearrangement of an α,β-Unsaturated Ester and Stereodivergent Intramolecular SN2′ Reaction: Development and Application to the Total Synthesis of Sphingofungin F
Authors: Sugai Tomoya , Usui Shunme , Tsuzaki Shun , Oishi Hiroki , Yasushima Daichi , Hisada Shoko , Fukuyasu Takahiro , Oishi Takeshi , Sato Takaaki , Chida Noritaka 
Published: January 2018

AbstractThe development of a two-step synthesis for β-hydroxy-α,α-disubstituted amino acid derivatives from cyclic orthoamide is reported. The first step is the orthoamide-type Overman rearrangement of an α,β-unsaturated ester to give a sterically hindered α,α-disubstituted amidoester. The α,β-unsaturated ester is known to be a challenging substrate in the conventional Overman rearrangement due to the competitive aza-Michael reaction. However, suppression of the aza-Michael reaction is realized by two factors; 1) the high reaction temperature, and 2) an alkyl substituent at the α-position. The second step is stereodivergent intramolecular SN2′ reaction for the installation of a hydroxy group at the β-position. Either syn- or anti-type SN2′ reaction is possible by simply changing the reaction conditions. The developed method can provide all four possible stereoisomers of the β-hydroxy-α,α-disubstituted amino acid, and is successfully applied to the total synthesis of sphingofungin F.
Effects of stress or infection on rat behavior show robust reversals due to environmental disturbance
Authors: Abdulai-Saiku Samira , Hegde Akshaya , Vyas Ajai , Mitra Rupshi 
Published: January 2018

Background: The behavior of animals is intricately linked to the environment; a relationship that is often studied in laboratory conditions by using environmental perturbations to study biological mechanisms underlying the behavioral change. Methods: This study pertains to two such well-studied and well-replicated perturbations, i.e., stress-induced anxiogenesis and Toxoplasma gondii -induced loss of innate fear. Here, we demonstrate that behavioral outcomes of these experimental manipulations are contingent upon the ambient quality of the wider environment where animal facilities are situated. Results: During late 2014 and early 2015, a building construction project started adjacent to our animal facility. During this phase, we observed that maternal separation stress caused anxiolysis, rather than historically observed anxiogenesis, in laboratory rats. We also found that Toxoplasma gondii infection caused an increase, rather than historically observed decrease, in innate aversion to predator odors in rats. Conclusion: These observations suggest that effects of stress and Toxoplasma gondii are dependent on variables in the environment that often go unreported in the published literature.
Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor
Authors: Eliseev Igor E. , Yudenko Anna N. , Vysochinskaya Vera V. , Svirina Anna A. , Evstratyeva Anna V. , Drozhzhachih Maria S. , Krendeleva Elena A. , Vladimirova Anna K. , Nemankin Timofey A. , Ekimova Viktoria M. , Ulitin Andrey B. , Lomovskaya Maria I. , Yakovlev Pavel A. , Bukatin Anton S. , Knyazev Nickolay A. , Moiseenko Fedor V. , Chakchir Oleg B. 
Published: January 2018

Background: The ability of ErbB3 receptor to functionally complement ErbB1-2 and induce tumor resistance to their inhibitors makes it a unique target in cancer therapy by monoclonal antibodies. Here we report the expression, purification and structural analysis of a new anti-ErbB3 single-chain antibody. Methods: The VHH fragment of the antibody was expressed in E. coli SHuffle cells as a SUMO fusion, cleaved by TEV protease and purified to homogeneity. Binding to the extracellular domain of ErbB3 was studied by surface plasmon resonance. For structural studies, the antibody was crystallized by hanging-drop vapor diffusion in two different forms. Results: We developed a robust and efficient system for recombinant expression of single-domain antibodies. The purified antibody was functional and bound ErbB3 with KD = 1 μM. The crystal structures of the VHH antibody in space groups C2 and P1 were solved by molecular replacement at 1.6 and 1.9 Å resolution. The high-quality electron density maps allowed us to build precise atomic models of the antibody and the putative paratope. Surprisingly, the CDR H2 existed in multiple distant conformations in different crystal forms, while the more complex CDR H3 had a low structural variability. The structures were deposited under PDB entry codes 6EZW and 6F0D. Conclusions: Our results may facilitate further mechanistic studies of ErbB3 inhibition by single-chain antibodies. Besides, the solved structures will contribute to datasets required to develop new computational methods for antibody modeling and design.
ANALISIS PREFERENSI DAN PROSPEKTIF PARTSIPIPATIF DALAM PERENCANAAN PENATAAN DAN PENYESUAIAN ULANG LAHAN (LAND READJUSTMENT) KAWASAN KAMPUNG BRAGA BANDUNG
Authors: Wihadanto Ake , Barus Baba , Achsani Noer Azam , Bratakusumah Deddy S. 
Published: January 2018

This research is purported to understand and map people’s preferences on rearrangement plan of the area. General description of people’s preferences is resulted by using qualitative descriptive analysis on data gained from interview and FGD. Furthermore, by employing Participatory Prospective Analysis (PPA) the people’s preferences has represented through the following key variables, those are transparency, people’s bargaining position, tenurial (ownership) system, communication, land value, institution/organization, location’s economic value, and level of conflict potential. Based on those variables, the future’s scenarios are constructed as follows: (1) Status quo; (2) Negative; (3) Positive; and (4) Progressive. The way to anticipate the first two scenarios are to close or impede any room or possibilities of the scenarios’ emergence. Meanwhile, for the last two scenarios, the anticipation way is to promote or enhance the scenarios’ emergence, maintaining sustainability of the scenarios, as well as avoiding any ways that can reverse the scenarios’ direction. Both ways of anticipation should be carried out through transparency, communication, and institution.