bluuebunny/crossref_metadata_2025_split huggingface dataset:
exKidneyBERT: a language model for kidney transplant pathology reports and the crucial role of extended vocabularies
Authors: Yang Tiancheng , Sucholutsky Ilia , Jen Kuang-Yu , Schonlau Matthias 
Published: February 2024

Background
Pathology reports contain key information about the patient’s diagnosis as well as important gross and microscopic findings. These information-rich clinical reports offer an invaluable resource for clinical studies, but data extraction and analysis from such unstructured texts is often manual and tedious. While neural information retrieval systems (typically implemented as deep learning methods for natural language processing) are automatic and flexible, they typically require a large domain-specific text corpus for training, making them infeasible for many medical subdomains. Thus, an automated data extraction method for pathology reports that does not require a large training corpus would be of significant value and utility.

Objective
To develop a language model-based neural information retrieval system that can be trained on small datasets and validate it by training it on renal transplant-pathology reports to extract relevant information for two predefined questions: (1) “What kind of rejection does the patient show?”; (2) “What is the grade of interstitial fibrosis and tubular atrophy (IFTA)?”

Methods
Kidney BERT was developed by pre-training Clinical BERT on 3.4K renal transplant pathology reports and 1.5M words. Then, exKidneyBERT was developed by extending Clinical BERT’s tokenizer with six technical keywords and repeating the pre-training procedure. This extended the model’s vocabulary. All three models were fine-tuned with information retrieval heads.

Results
The model with extended vocabulary, exKidneyBERT, outperformed Clinical BERT and Kidney BERT in both questions. For rejection, exKidneyBERT achieved an 83.3% overlap ratio for antibody-mediated rejection (ABMR) and 79.2% for T-cell mediated rejection (TCMR). For IFTA, exKidneyBERT had a 95.8% exact match rate.

Conclusion
ExKidneyBERT is a high-performing model for extracting information from renal pathology reports. Additional pre-training of BERT language models on specialized small domains does not necessarily improve performance. Extending the BERT tokenizer’s vocabulary library is essential for specialized domains to improve performance, especially when pre-training on small corpora.
Effect of lag screw on stability of first metatarsophalangeal joint arthrodesis with medial plate
Authors: Daszkiewicz Karol , Rucka Magdalena , Czuraj Krzysztof , Andrzejewska Angela , Łuczkiewicz Piotr 
Published: February 2024

Background
First metatarsophalangeal joint (MTP-1) arthrodesis is a commonly performed procedure in the treatment of disorders of the great toe. Since the incidence of revision after MTP-1 joint arthrodesis is not insignificant, a medial approach with a medially positioned locking plate has been proposed as a new technique. The aim of the study was to investigate the effect of the application of a lag screw on the stability and strength of first metatarsophalangeal joint arthrodesis with medial plate.

Methods
The bending tests in a testing machine were performed for models of the first metatarsal bone and the proximal phalanx printed on a 3D printer from polylactide material. The bones were joined using the locking titanium plate and six locking screws. The specimens were divided into three groups of seven each: medial plate and no lag screw, medial plate with a lag screw, dorsal plate with a lag screw. The tests were carried out quasi-static until the samples failure.

Results
The addition of the lag screw to the medial plate significantly increased flexural stiffness (41.45 N/mm vs 23.84 N/mm, p = 0.002), which was lower than that of the dorsal plate with a lag screw (81.29 N/mm, p < 0.001). The similar maximum force greater than 700 N (p > 0.50) and the relative bone displacements lower than 0.5 mm for a force of 50 N were obtained for all fixation techniques.

Conclusions
The lag screw significantly increased the shear stiffness in particular and reduced relative transverse displacements to the level that should not delay the healing process for the full load of the MTP-1 joint arthrodesis with the medial plate. It is recommended to use the locking screws with a larger cross-sectional area of the head to minimize rotation of the medial plate relative to the metatarsal bone.
Use of Callistemon citrinus as a gastroprotective and anti-inflammatory agent on indomethacin-induced gastric ulcers in obese rats
Authors: Piñón-Simental Jonathan Saúl , Ayala-Ruiz Luis Alberto , Ortega-Pérez Luis Gerardo , Magaña-Rodríguez Oliver Rafid , Meléndez-Herrera Esperanza , Aguilera-Méndez Asdrubal , Rios-Chavez Patricia 
Published: February 2024

Background
Obesity leads to an elevated risk of developing gastrointestinal disease such as gastric ulcers. Callistemon citrinus leaf extract has shown antioxidant, antimicrobial, hepatoprotective, and chemoprotective effects against colon cancer. The aim of this study is to evaluate the gastroprotective effect of C. citrinus leaf extract on indomethacin-induced gastric ulcers in obese rats.

Methods
Gastric ulcers were induced in female obese Wistar rats using a single oral dose of indomethacin (IND). In the first stage, the rats were fed with a high fat sugar diet (HFSD) for 15 weeks to induce obesity and, at the same time, the diet of the other group of animals included daily administration of ethanolic C. citrinus leaf extract (250 mg/kg) in addition to HFSD. In the second stage, gastric ulcers were induced with IND (30 mg/kg). The gastroprotective activity of C. citrinus, the inflammatory enzyme activities, and cytokines in the stomach were determined.

Results
C. citrinus produced a reduction of gastric lesions caused by IND. Myeloperoxidase (MPO), cyclooxygenase-2 (COX-2), and 5-lipoxygenase (5-LOX) activities also decreased. Although inflammatory biomarkers such as TNFα, IL-6, AOPP, and leptin were significantly decreased by C. citrinus, adiponectin levels increased. Moreover, C. citrinus decreased weight gain and morphological and biochemical parameters.

Conclusion
The use of indomethacin in rats fed with a high fat-sugar diet increased gastric ulcers. Gastroprotective effect of C. citrinus in obese rats is attributed to the reduction of pro-inflammatory cytokines and the inflammatory enzymes.
Prognostic factors and outcomes of invasive pulmonary aspergillosis, a retrospective hospital-based study
Authors: Chen Wei-Che , Chen I-Chieh , Chen Jun-Peng , Liao Tsai-Ling , Chen Yi-Ming 
Published: February 2024

Objective
Invasive pulmonary aspergillosis (IPA) affects immunocompromised hosts and is associated with higher risks of respiratory failure and mortality. However, the clinical outcomes of different IPA types have not been identified.

Methods
Between September 2002 and May 2021, we retrospectively enrolled patients with IPA in Taichung Veterans General Hospital, Taiwan. Cases were classified as possible IPA, probable IPA, proven IPA, and putative IPA according to EORTC/MSGERC criteria and the AspICU algorithm. Risk factors of respiratory failure, kidney failure, and mortality were analyzed by logistic regression. A total of 3-year survival was assessed by the Kaplan-Meier method with log-rank test for post-hoc comparisons.

Results
We included 125 IPA patients (50: possible IPA, 47: probable IPA, 11: proven IPA, and 17: putative IPA). Comorbidities of liver cirrhosis and solid organ malignancy were risk factors for respiratory failure; diabetes mellitus and post-liver or kidney transplantation were related to kidney failure. Higher galactomannan (GM) test optical density index (ODI) in either serum or bronchoalveolar lavage fluid was associated with dismal outcomes. Probable IPA and putative IPA had lower 3-year respiratory failure-free survival compared to possible IPA. Probable IPA and putative IPA exhibited lower 3-year renal failure-free survival in comparison to possible IPA and proven IPA. Putative IPA had the lowest 3-year overall survival rates among the four IPA groups.

Conclusion
Patients with putative IPA had higher mortality rates than the possible, probable, or proven IPA groups. Therefore, a prompt diagnosis and timely treatment are warranted for patients with putative IPA.
Synthesis of β‐L‐2′‐Deoxythymidine (L‐dT)
Authors: Pierra Claire , Dukhan David , Gosselin Gilles , Sommadossi Jean‐Pierre 
Published: April 2006

AbstractThe “unnatural” l‐nucleoside β‐l‐2′‐deoxythymidine (L‐dT) is a potent, specific, and selective inhibitor of the replication of hepatitis B virus (HBV), which is currently in Phase III clinical trials. This unit describes, in detail, a semi‐large‐scale synthesis of l‐dT. This convenient methodology produces l‐dT in six steps starting with l‐ribose and ending with a satisfactory overall yield of l‐dT, and may be applied to other 2′‐deoxynucleosides, incorporating different heterocyclic bases.
The Importance of Biological Databases in Biological Discovery
Authors: Baxevanis Andreas D. 
Published: April 2006

AbstractBiological databases play a central role in bioinformatics. They offer scientists the opportunity to access sequence and structure data for tens of thousands of sequences from a broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, UCSC Genome Browser, and Ensembl. Model organism databases, including the TIGR Gene Indices, WormBase, and the Arabidopsis Information Resource (TAIR) are also covered. Non‐sequence‐centric databases such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) are also discussed.
Searching the NCBI Databases Using Entrez
Authors: Baxevanis Andreas D. 
Published: April 2006

AbstractOne of the most widely‐used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An builds upon the first Basic Protocol, using additional, built‐in features of the Entrez system, and providing alternative ways to issue the initial query. The reviews how to save frequently‐issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.
PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature
Authors: Yoo Danny , Xu Iris , Berardini Tanya Z. , Yon Rhee Seung , Narayanasamy Vijay , Twigger Simon 
Published: April 2006

AbstractFor most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.
Raw Materials and Energy
Authors: Kola Rolf , von Elsner Otto , Riepe Wolfgang , Reuter Knud 
Published: April 2006

AbstractThe article contains sections titled:1.Introduction2.Mineral Raw Materials2.1.Formation of Deposits2.2.Mineralogy and Raw Material Groups2.3.Development of Deposits2.4.Exploitation of Raw Materials2.5.Availability of Mineral Raw Materials2.6.Environmental Factors in the Processing of Raw Materials2.7.Secondary Raw Materials3.Oil, Gas, and Coal3.1.Introduction3.2.Oil3.2.1.Exploration3.2.2.Production3.2.3.Transportation3.2.4.Loading and Storage3.2.5.Processing3.2.6.Uses3.2.7.Cost3.3.Gas3.3.1.Processing3.3.2.Transportation3.3.3.Storage3.3.4.Uses3.3.5.Cost3.4.Coal3.4.1.Mining Engineering3.4.2.Processing3.4.3.Utilization4.Renewable Resources4.1.Significance4.2.Important Renewable Resources4.3.Industrial Use4.3.1.Natural Fats and Oils4.3.2.Cellulose and Its Derivatives4.3.2.1.Cellulose4.3.2.2.Cellulose Esters4.3.2.3.Cellulose Ethers4.3.3.Starch4.3.4.Low‐Molecular Carbohydrates – Sugars4.3.5.Other Renewable Resources4.3.5.1.Polyisoprene4.3.5.2.Natural Resins4.3.5.3.Plant Polysaccharides (“Gums”)4.3.5.4.Active Substances Based on Renewable Resources4.3.5.5.Flavors and Fragrances4.4.Energy Use4.4.1.Biofuels4.4.2.Biogas4.4.3.Heat from Biomass4.5.Appraisal4.5.1.Ecobalancing of Renewable Resources4.5.2.Opportunities and Limits of Use of Renewable Resources
Inside Front Cover: Trilayered Ceramic–Metal–Polymer Microcantilevers with Dramatically Enhanced Thermal Sensitivity (Adv. Mater. 9/2006)
Authors: Lin Y.‐H. , McConney M. E. , LeMieux M. C. , Peleshanko S. , Jiang C. , Singamaneni S. , Tsukruk V. V. 
Published: April 2006

AbstractA novel trilayered (ceramic–metal–polymer) design for highly sensitive, thermally responsive microcantilever arrays is reported on p. 1157 by Tsukruk and co‐workers. In this design, the topmost nanocomposite layer, reinforced with carbon nanotubes and silver nanoparticles, acts as a strong thermal‐stress‐driven actuator to enhance conventional biomaterial performance. These polymer–metal–ceramic microcantilevers with enhanced (fourfold) thermal sensitivity may serve as a basis for the next generation of uncooled thermal microsensor arrays because of outstanding thermal and spatial resolution.
Enantiophore modeling in 3D‐QSAR. A data mining application on Whelk‐O1 chiral stationary phase
Authors: Rio Alberto Del , Piras Patrick , Roussel Christian 
Published: April 2006

AbstractA combination of the enantiophore concept described in a previous study and a quantitative structure enantioselective relationship (QSER) based on partial least squares (PLS) analysis is presented. In the present study, a comprehensive approach for describing the enantioselective binding properties of the Whelk‐O1 chiral HPLC receptor is achieved using molecular descriptors calculated by the GRID program. The GRID descriptors allow us to describe the molecules in terms of their ability to form favorable interactions with independent chemical groups (probes) that can be related to receptor sites. For each molecule, we compute 120 enantiophore descriptors representing the energy contributions from all possible pairwise combinations of probes. The overall procedure was simplified by considering only the most energetically favorable locations and converting selected grid‐point energies into alignment‐independent descriptors. By using a training set of 143 diverse chiral compounds, an optimal PLS model requiring seven components was chosen by using the cross‐validation method resulting in a correlation coefficient R2 = 0.88 and a cross validated correlation coefficient Q2 = 0.85. An interpretation of the model is proposed based upon a visual inspection of the regression coefficient plots. From these plots, the influence of particular molecular features for selective binding of solutes was estimated and used to outline the chiral recognition sites in the Whelk‐O1 receptor. The predictive power of our model has been estimated by means of an external data set emphasizing the suitability of the procedure also for predictive aims. Chirality 18:498–508, 2006. © 2006 Wiley‐Liss, Inc.
Vancomycin as chiral selector for enantioselective separation of selected profen nonsteroidal anti‐inflammatory drugs incapillary liquid chromatography
Authors: Kafková Boz̆ena , Bosáková Zuzana , Tesar̆ová Eva , Coufal Pavel , Messina Antonella , Sinibaldi Massimo 
Published: April 2006

AbstractThe chiral selector vancomycin was used either as mobile phase additive or bound as a chiral stationary phase (CSP) for the stereoselective separation of seven racemic nonsteroidal anti‐inflammatory drugs (NSAIDs), fenoprofen, carprofen, flurbiprofen, indoprofen, flobufen, ketoprofen, and suprofen, by capillary liquid chromatography. The effect of the type of stationary phase, the chiral column Chirobiotic V or the achiral stationary phases Nucleosil 100 C8 HD and Nucleosil 100 C18 HD, and the concentration of vancomycin in the mobile phase on separation of the drug enantiomers were evaluated. All the drugs, except flobufen, were successfully enantioseparated on Nucleosil 100 C8 HD with 4 mM vancomycin present in the mobile phase (composed of methanol and buffer) in the reversed phase mode. On the vancomycin‐bonded chiral stationary phase, it was difficult to get enantioseparations of the profen NSAIDs. However, flobufen gave better enantioseparation on the vancomycin CSP. The better enantioresolution of the majority of profen derivatives on the achiral columns with vancomycin added to the mobile phase can be attributed in particular to the higher separation efficiency of this capillary chromatographic system. In addition, vancomycin dimers, formed in the mobile phase, seem to offer a better steric arrangement for stereoselective interaction to these analytes than the vancomycin bonded on the CSP. These substantial differences in the CS structure significantly influence the chiral discrimination mechanism. Chirality 18:531–538, 2006. © 2005 Wiley‐Liss, Inc.
Smoking affects treatment outcome in patients with advanced nonsmall cell lung cancer
Authors: Tsao Anne S. , Liu Diane , Lee J. Jack , Spitz Margaret , Hong Waun Ki 
Published: April 2006

AbstractBACKGROUNDThe purpose of the current study was to determine whether smoking during chemotherapy or chemoradiation therapy for nonsmall cell lung cancer (NSCLC) affects treatment outcome.METHODSThe authors reviewed the medical records of patients with NSCLC (AJCC Stage III or IV) who were treated with frontline chemotherapy or chemoradiation therapy at the University of Texas M. D. Anderson Cancer Center between January 1993 and December 2002. Treatment type, response, progression‐free survival, and overall survival (OS) were correlated with patient demographic characteristics, clinical features, and smoking habits at the time of diagnosis and during therapy.RESULTSOf 1370 patients who were eligible for analysis, 497 received chemoradiation therapy and 873 received chemotherapy. In the chemoradiation group, 6% of patients were never‐smokers, 45% were former smokers, and 49% were current smokers. Multivariate analysis demonstrated no prognostic effect of smoking status on treatment response or OS rates in the chemoradiation therapy group. In the chemotherapy group, 16% of patients were never‐smokers, 42% were former smokers, and 42% were current smokers; 20% of patients continued to smoke during therapy. Never‐smokers had higher response rates (19% vs. 8% vs. 12%; P = .004) and lower rates of progressive disease (49% vs. 65% vs. 66%; P = .002) than former and current smokers, respectively. The OS rates were found to be higher among never‐smokers (P <.0001), women (P = .002), and those with a better Eastern Cooperative Oncology Group (ECOG) performance status (P <.0001). The multivariate Cox model indicated that with adjustment for age, gender, stage of disease, and ECOG performance status, the hazard ratio was 1.47 for former smokers (P = .003) and 1.55 for current smokers (P = .0004). Active smoking during therapy did not appear to impact outcome.CONCLUSIONSNever‐smokers were found to have an improved outcome over smokers when treated with chemotherapy. Cancer 2006. © 2006 American Cancer Society.
Associations between juvenile delinquency and weight‐related variables: Analyses from a national sample of high school students
Authors: Ho Ching‐hua , Kingree J. B. , Thompson Martie P. 
Published: April 2006

AbstractObjective:This study examined direct and conditional associations between juvenile delinquency and weight‐related variables in a national sample of high school students.Method:Data from the 2003 Youth Risk Behavior Survey (YRBS) of 12,713 high school students aged 14 to 17 were examined. Logistic regression analyses were used to analyze the data.Results:Bivariate and multivariate analyses indicated that juvenile delinquents were more likely than nondelinquents to use fasting, vomiting, and drugs to lose weight or to keep from gaining weight. Multivariate analyses also showed that delinquents were more likely than nondelinquents to perceive themselves as overweight, but the two groups did not differ in regard to actual overweight status. Tests of interactions in multivariate analyses indicated that the associations between delinquent status and specific, weight‐related variables were stronger among younger than among older adolescents, as well as among female than among male adolescents.Conclusions:Future research should examine risk and protective factors for unhealthy weight control behaviors and perceptions among delinquents. © 2006 by Wiley Periodicals, Inc. Int J Eat Disord 2006
Oxidation of Electrodeposited Copper on Boron Doped Diamond in Acidic Solution: Manipulating the Size of Copper Nanoparticles Using Voltammetry
Authors: Welch Christine M. , Simm Andrew O. , Compton Richard G. 
Published: April 2006

AbstractThe in situ deposition of copper, in acidic solution onto a Boron Doped Diamond electrode, using cyclic voltammetry is explored and produced surfaces are imaged using Atomic Force Microscopy. A uniformly dense covering of copper nanoparticles is produced when the potential of a freshly polished BDD electrode is swept from 0 V in a negative direction. For example, in 1 M H2SO4 with a Cu(II) concentration of 1 mM, nanoparticles of height 10.1 nm, diameter 74.6 nm and a density of 16.1 particles per μm2 are created when the potential is swept to −0.35 V. The higher the concentration of Cu(II) in solution or the larger the magnitude of the end potential the larger the nanoparticles are and the more densely they are spread. When the direction of the scan is reversed and a positive potential sweep carried out evidence from the observed cyclic voltammograms and AFM images shows that copper is being incompletely stripped from the electrode surface. If the potential is then cycled continuously ten times, as would happen when the process is used for electroanalytical purposes, then an irregular and irreproducible deposit is observed. One can infer from this evidence that the incompletely stripped copper is electrochemically active and therefore adversely affecting subsequent deposition processes. Comparison to existing literature shows that the discrete application of particular deposition and stripping potentials is a much better way to produce a deposit of copper nanoparticles than application of potential through cyclic voltammetry.