bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comorbidities and Charlson score in resected stage I nonsmall cell lung cancer
Authors: Moro-Sibilot D. , Aubert A. , Diab S. , Lantuejoul S. , Fourneret P. , Brambilla E. , Brambilla C. , Brichon P. Y. 
Published: August 2005

Patients with nonsmall cell lung cancer (NSCLC) have been shown to have a higher prevalence of comorbidity associated with age and tobacco consumption. The objective of the present study was to determine the impact of comorbidity on survival after surgery of stage I NSCLC.In total, 588 consecutive patients operated on for a pathological stage I NSCLC between January 1, 1979 and December 31, 2003 were studied. Comorbidities were analysed individually. Overall comorbidity was assessed using the Charlson index of comorbidity (CCI). Survival data were collected for each patient from the date of operation, with a median duration of follow-up of 104 months. Survival analyses and Cox proportional hazards model analyses were used.The mean age of patients was 62.7 yrs, and 529 (89%) patients were male. The distribution of overall comorbidity severity was as follows. CCI grade 0: 47.1%; grade 1–2: 43.7%; grade 3–4: 8.3%; and grade ≥5: 0.8%.The 2, 3 and 5 yrs survival were 69, 62 and 50%, respectively. Multivariable analysis showed that T stage, age, a concomitant history of moderate-to-severe liver disease, a past history of cured cancer, cerebrovascular disease and CCI were independent predictors of survival (Hazard Ratio for CCI grade >2: 1.81; 95% confidence interval 1.25–2.63).In conclusion, comorbidity has a significant impact on survival after surgical resection of patients with stage I nonsmall cell lung cancer. The use of a validated index of comorbidity in prognostic analyses of resected nonsmall cell lung cancer is recommended.
Leukotriene D4-induced hypoxaemia in asthma is mediated by the cys-leukotriene1receptor
Authors: Casas A. , Gómez F. P. , Dahlén B. , Roca J. , Barberà J. A. , Dahlén S-E. , Rodríguez-Roisin R. 
Published: August 2005

Bronchoprovocation with cysteinyl-leukotrienes (LTs) induces airflow obstruction and gas exchange abnormalities, namely ventilation-perfusion ratio (V′A/Q′) imbalance. However, it is unknown which of the two different receptors for cysteinyl-LTs mediate theseV′A/Q′ disturbances.In a double-blinded, crossover design, 10 patients with mild asthma were randomised to receive an oral single dose of the selective cysteinyl-LT1receptor antagonist montelukast (40 mg) or placebo before leukotriene (LT)D4inhalation challenge. Gas exchange, includingV′A/Q′ descriptors were measured at baseline, 3 h after montelukast/placebo pretreatment and 5, 15 and 45 min after the LTD4challenge.Compared with montelukast, inhalation of LTD4induced a marked fall in forced expiratory volume in one second (mean±se33±2%) and profoundV′A/Q′ mismatching, reflected by a decreased arterial oxygen tension (from 100±4 to 75±3 mmHg) and an increased overall index ofV′A/Q′ heterogeneity dispersion of retention minus excretion inert gases corrected for dead space (from 4.9±1.2 to 8.4±1.1; normal≤3.0; dimensionless), 5 min after placebo. Following montelukast, LTD4produced no significant changes in any of the variables.In conclusion, these findings point to the view that leukotriene D4-induced gas exchange disturbances and bronchoconstriction are both mediated by the cysteinyl-leukotriene1receptor.
A prediction rule for clinical diagnosis of severe acute respiratory syndrome
Authors: Ho P. L. , Chau P. H. , Yip P. S. F. , Ooi G. C. , Khong P. L. , Ho J. C. , Wong P. C. , Ko C. , Yan C. , Tsang K. W. 
Published: August 2005

A prospective study was undertaken to identify clinical, radiographical, haematological and biochemical profiles of severe acute respiratory syndrome (SARS) patients.A prediction rule, which demarcates low from high risk patients for SARS in an outbreak situation was developed. A total of 295 patients with unexplained respiratory illnesses, admitted to Queen Mary Hospital, Hong Kong SAR, China, in March to July 2003, were evaluated for clinical, radiological, haematological and alanine transaminase (ALT) data daily for 3 days after hospitalisation.In total, 44 cases were subsequently confirmed to have SARS by RT-PCR (68.2%) and serology (100%). The scoring system of attributing 11, 10, 3, 3 and 3 points to the presence of independent risk factors, namely: epidemiological link, radiographical deterioration, myalgia, lymphopenia and elevated ALT respectively, generated high and low-risk (total score 11–30 and 0–10, respectively) groups for SARS. The sensitivity and specificity of this prediction rule in positively identifying a SARS patient were 97.7 and 81.3%, respectively. The positive and negative predictive values were 47.8 and 99.5%, respectively.The prediction rule appears to be helpful in assessing suspected patients with severe acute respiratory syndrome at the bedside, and should be further validated in other severe acute respiratory syndrome cohorts.
Automation of gene assignments to metabolic pathways using high-throughput expression data
Authors: Popescu Liviu , Yona Golan 
Published: August 2005

Abstract
Background
Accurate assignment of genes to pathways is essential in order to understand the functional role of genes and to map the existing pathways in a given genome. Existing algorithms predict pathways by extrapolating experimental data in one organism to other organisms for which this data is not available. However, current systems classify all genes that belong to a specific EC family to all the pathways that contain the corresponding enzymatic reaction, and thus introduce ambiguity.

Results
Here we describe an algorithm for assignment of genes to cellular pathways that addresses this problem by selectively assigning specific genes to pathways. Our algorithm uses the set of experimentally elucidated metabolic pathways from MetaCyc, together with statistical models of enzyme families and expression data to assign genes to enzyme families and pathways by optimizing correlated co-expression, while minimizing conflicts due to shared assignments among pathways. Our algorithm also identifies alternative ("backup") genes and addresses the multi-domain nature of proteins.
We apply our model to assign genes to pathways in the Yeast genome and compare the results for genes that were assigned experimentally. Our assignments are consistent with the experimentally verified assignments and reflect characteristic properties of cellular pathways.

Conclusion
We present an algorithm for automatic assignment of genes to metabolic pathways. The algorithm utilizes expression data and reduces the ambiguity that characterizes assignments that are based only on EC numbers.
Reduction of the hand representation in the ipsilateral primary motor cortex following unilateral section of the corticospinal tract at cervical level in monkeys
Authors: Schmidlin Eric , Wannier Thierry , Bloch Jocelyne , Belhaj-Saif Abderraouf , Wyss Alexander F , Rouiller Eric M 
Published: August 2005

Abstract

Background
After sub-total hemi-section of cervical cord at level C7/C8 in monkeys, the ipsilesional hand exhibited a paralysis for a couple of weeks, followed by incomplete recovery of manual dexterity, reaching a plateau after 40–50 days. Recently, we demonstrated that the level of the plateau was related to the size of the lesion and that progressive plastic changes of the motor map in the contralesional motor cortex, particularly the hand representation, took place following a comparable time course. The goal of the present study was to assess, in three macaque monkeys, whether the hand representation in the ipsilesional primary motor cortex (M1) was also affected by the cervical hemi-section.

Results
Unexpectedly, based on the minor contribution of the ipsilesional hemisphere to the transected corticospinal (CS) tract, a considerable reduction of the hand representation was also observed in the ipsilesional M1. Mapping control experiments ruled out the possibility that changes of motor maps are due to variability of the intracortical microstimulation mapping technique. The extent of the size reduction of the hand area was nearly as large as in the contralesional hemisphere in two of the three monkeys. In the third monkey, it represented a reduction by a factor of half the change observed in the contralesional hemisphere. Although the hand representation was modified in the ipsilesional hemisphere, such changes were not correlated with a contribution of this hemisphere to the incomplete recovery of the manual dexterity for the hand affected by the lesion, as demonstrated by reversible inactivation experiments (in contrast to the contralesional hemisphere). Moreover, despite the size reduction of M1 hand area in the ipsilesional hemisphere, no deficit of manual dexterity for the hand opposite to the cervical hemi-section was detected.

Conclusion
After cervical hemi-section, the ipsilesional motor cortex exhibited substantial reduction of the hand representation, whose extent did not match the small number of axotomized CS neurons. We hypothesized that the paradoxical reduction of hand representation in the ipsilesional hemisphere is secondary to the changes taking place in the contralesional hemisphere, possibly corresponding to postural adjustments and/or re-establishing a balance between the two hemispheres.
Neuromagnetic brain responses to words from semantic sub- and supercategories
Authors: Assadollahi Ramin , Rockstroh Brigitte 
Published: August 2005

Abstract
Background
We explored spatio-temporal patterns of cortical activity evoked by written words from super-ordinate and sub-ordinate semantic categories and hoped to find a differential cortical and/or temporal distribution of the brain response depending on the level of the categories. Twenty-three subjects saw 360 words belonging to six sub-ordinate categories (mammals, birds, fish, fruit, flowers, trees) within two super-ordinate categories (fauna, flora). Visually evoked magnetic fields were determined from whole-head (148-sensor) magnetoencephalography and analyzed in the source space (Minimum Norm Estimate).

Results
Activity (MNE amplitudes) 100–150 ms after stimulus onset in the left occipito-temporal area distinguished super-ordinate categories, while later activity (300–550 ms) in the left temporal area distinguished the six sub-ordinate categories.

Conclusion
Our results document temporally and spatially distinct processing and representation of words according to their categorical information. If further studies can rule out possible confounds then our results may help constructing a theory about the internal structure of entries in the mental lexicon and its access.
Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
Authors: Bräutigam Marcus , Lindlöf Angelica , Zakhrabekova Shakhira , Gharti-Chhetri Gokarna , Olsson Björn , Olsson Olof 
Published: September 2005

Abstract

Background
Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required.

Results
From an oat cDNA library 9792 single-pass EST sequences were obtained. The library was prepared from pooled RNA samples isolated from leaves of four-week old Avena sativa (oat) plants incubated at +4°C for 4, 8, 16 and 32 hours. Exclusion of sequences shorter than 100 bp resulted in 8508 high-quality ESTs with a mean length of 710.7 bp. Clustering and assembly identified a set of 2800 different transcripts denoted the Avena sativa cold induced UniGene set (AsCIUniGene set). Taking advantage of various tools and databases, putative functions were assigned to 1620 (58%) of these genes. Of the remaining 1180 unclassified sequences, 427 appeared to be oat-specific since they lacked any significant sequence similarity (Blast E values > 10-10) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX E values ≤ 10-10) to genes previously reported to be involved in cold stress related processes. 107 novel oat transcription factors were also identified, out of which 51 were similar to genes previously shown to be cold induced. The CBF transcription factors have a major role in regulating cold acclimation. Four oat CBF sequences were found, belonging to the monocot cluster of DREB family ERF/AP2 domain proteins. Finally in the total EST sequence data (5.3 Mbp) approximately 400 potential SSRs were found, a frequency similar to what has previously been identified in Arabidopsis ESTs.

Conclusion
The AsCIUniGene set will now be used to fabricate an oat biochip, to perform various expression studies with different oat cultivars incubated at varying temperatures, to generate molecular markers and provide tools for various genetic transformation experiments in oat. This will lead to a better understanding of the cellular biology of this important crop and will open up new ways to improve its agronomical properties.
Tracheal ring fracture and early tracheomalacia following percutaneous dilatational tracheostomy
Authors: Ho Eu Chin , Kapila Atul , Colquhoun-Flannery William 
Published: August 2005

Abstract

Background
Percutaneous dilatational tracheostomy (PDT) is increasingly popular within intensive care units for patients who need prolonged ventilatory support. Significant complications are rare.

Case presentation
Our patient suffered tracheal ring fracture and early tracheomalacia following this procedure. These complications are demonstrated in our accompanying video.

Conclusion
Contrary to common beliefs, tracheal rings are commonly fractured during the PDT procedure. The consequent granulation can lead to tracheal stenosis and tracheomalacia.
Automation of a problem list using natural language processing
Authors: Meystre Stephane , Haug Peter J 
Published: August 2005

Abstract

Background
The medical problem list is an important part of the electronic medical record in development in our institution. To serve the functions it is designed for, the problem list has to be as accurate and timely as possible. However, the current problem list is usually incomplete and inaccurate, and is often totally unused. To alleviate this issue, we are building an environment where the problem list can be easily and effectively maintained.

Methods
For this project, 80 medical problems were selected for their frequency of use in our future clinical field of evaluation (cardiovascular). We have developed an Automated Problem List system composed of two main components: a background and a foreground application. The background application uses Natural Language Processing (NLP) to harvest potential problem list entries from the list of 80 targeted problems detected in the multiple free-text electronic documents available in our electronic medical record. These proposed medical problems drive the foreground application designed for management of the problem list. Within this application, the extracted problems are proposed to the physicians for addition to the official problem list.

Results
The set of 80 targeted medical problems selected for this project covered about 5% of all possible diagnoses coded in ICD-9-CM in our study population (cardiovascular adult inpatients), but about 64% of all instances of these coded diagnoses. The system contains algorithms to detect first document sections, then sentences within these sections, and finally potential problems within the sentences. The initial evaluation of the section and sentence detection algorithms demonstrated a sensitivity and positive predictive value of 100% when detecting sections, and a sensitivity of 89% and a positive predictive value of 94% when detecting sentences.

Conclusion
The global aim of our project is to automate the process of creating and maintaining a problem list for hospitalized patients and thereby help to guarantee the timeliness, accuracy and completeness of this information.
Subjective assessments of comorbidity correlate with quality of life health outcomes: Initial validation of a comorbidity assessment instrument
Authors: Bayliss Elizabeth A , Ellis Jennifer L , Steiner John F 
Published: September 2005

Abstract

Background
Interventions to improve care for persons with chronic medical conditions often use quality of life (QOL) outcomes. These outcomes may be affected by coexisting (comorbid) chronic conditions as well as the index condition of interest. A subjective measure of comorbidity that incorporates an assessment of disease severity may be particularly useful for assessing comorbidity for these investigations.

Methods
A survey including a list of 25 common chronic conditions was administered to a population of HMO members age 65 or older. Disease burden (comorbidity) was defined as the number of self-identified comorbid conditions weighted by the degree (from 1 to 5) to which each interfered with their daily activities. We calculated sensitivities and specificities relative to chart review for each condition. We correlated self-reported disease burden, relative to two other well-known comorbidity measures (the Charlson Comorbidity Index and the RxRisk score) and chart review, with our primary and secondary QOL outcomes of interest: general health status, physical functioning, depression screen and self-efficacy.

Results
156 respondents reported an average of 5.9 chronic conditions. Median sensitivity and specificity relative to chart review were 75% and 92% respectively. QOL outcomes correlated most strongly with disease burden, followed by number of conditions by chart review, the Charlson Comorbidity Index and the RxRisk score.

Conclusion
Self-report appears to provide a reasonable estimate of comorbidity. For certain QOL assessments, self-reported disease burden may provide a more accurate estimate of comorbidity than existing measures that use different methodologies, and that were originally validated against other outcomes. Investigators adjusting for comorbidity in studies using QOL outcomes may wish to consider using subjective comorbidity measures that incorporate disease severity.
Neoadjuvant chemotherapy versus primary surgery in advanced ovarian carcinoma
Authors: Hegazy Mohamed AF , Hegazi Refaat AF , Elshafei Mohamed A , Setit Ahmed E , Elshamy Maged R , Eltatoongy Mohamed , Halim Amal AF 
Published: August 2005

Abstract

Background
Patients with advanced ovarian cancer should be treated by radical debulking surgery aiming at complete tumor resection. Unfortunately about 70% of the patients present with advanced disease, when optimal debulking can not be obtained, and therefore these patients gain little benefit from surgery. Neoadjuvant chemotherapy (NACT) has been proposed as a novel therapeutic approach in such cases. In this study, we report our results with primary surgery or neoadjuvant chemotherapy as treatment modalities in the specific indication of operable patients with advanced ovarian carcinoma (no medical contraindication to debulking surgery).

Patients and methods
A total of 59 patients with stage III or IV epithelial ovarian carcinomas were evaluated between 1998 and 2003. All patients were submitted to surgical exploration aiming to evaluate tumor resectability. Neoadjuvant chemotherapy was given (in 27 patients) where optimal cytoreduction was not feasible. Conversely primary debulking surgery was performed when we considered that optimal cytoreduction could be achieved by the standard surgery (32 patients).

Results
Optimal cytoreduction was higher in the NACT group (72.2%) than the conventional group (62.4%), though not statistically significant (P = 0.5). More important was the finding that parameters of surgical aggressiveness (blood loss rates, ICU stay and total hospital stay) were significantly lower in NACT group than the conventional group. The median overall survival time was 28 months in the conventional group and 25 months in NACT group with a P value of 0.5. The median disease free survival was 19 months in the conventional group and 21 months in NACT group (P = 0.4). In multivariate analysis, the pathologic type and degree of debulking were found to affect the disease free survival significantly. Overall survival was not affected by any of the study parameters.

Conclusion
Primary chemotherapy followed by interval debulking surgery in select group of patients doesn't appear to worsen the prognosis, but it permits a less aggressive surgery to be performed.
Transfer of efficient anti-melanocyte T cells from vitiligo donors to melanoma patients as a novel immunotherapeutical strategy
Authors: Palermo Belinda , Garbelli Silvia , Mantovani Stefania , Giachino Claudia 
Published: August 2005

AbstractBackgroundVitiligo is a relatively common progressive depigmentary condition that is believed to be due to the autoimmune-mediated loss of epidermal melanocytes. High frequencies of self-reactive T lymphocytes directed toward melanocyte differentiation antigens are found in vitiligo patients and might be directly responsible for the pathogenesis of the disease. An interesting aspect of vitiligo is its relation to melanoma: cytotoxic T lymphocytes directed to self antigens shared by normal melanocytes and melanoma cells are found in both conditions, but the resulting immune reactions are completely different. From this standpoint, the selective destruction of pigment cells that occurs in cases of vitiligo is the therapeutic goal sought in melanoma research.Presentation of the hypothesisOur working hypothesis is that vitiligo patients might represent a unique source of therapeutic cells to be used in allo-transfer for HLA-matched melanoma patients. The adoptive transfer ofex-vivogenerated autologous tumor-specific T cells is a therapy that has met with only limited success, essentially because of inability to isolate therapeutically valuable T cells from the majority of tumor patients. Ideally, model systems where strong and efficient responses against the same (tumor) antigens are achieved would represent a better source of therapeutic cells. We believe it is possible to identify one such model in the melanoma-vitiligo dichotomy: T lymphocytes specific for different melanocyte differentiation antigens are found in vitiligo and represent the effective anti-melanocyte reactivity that is often ineffective in melanoma.Testing the hypothesisMelanocyte-specific T cell clones can be isolated from the peripheral blood of vitiligo patients and tested for their capacity to efficiently expandin vitrowithout loosing their cytotoxic activity and to migrate to the skin. Cytotoxicity against melanoma patients' non-tumor cells can also be tested. In addition, it would be interesting to attempt an in vivo animal model. If the results obtained from these validation steps will be satisfactory, it might be possible to plan the clinical grade preparation of relevant clones for transfer.Implications of the hypothesisWhen translated into a clinical trial, the possibility ofin vitroselecting few effective tumor-specific T cell clones for infusion, inherent with this approach, could enhance the therapeutic graft-versus-tumor effect while possibly decreasing the risk of graft-versus-host disease.