Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Comparative Structures in Biomedical Text

Comparison sentences are very commonly used by authors in biomedical literature to report results of experiments. In such comparisons, authors typically make observations under two different scenarios. In this paper, we present a system to automatically identify such comparative sentences and their components i.e. the compared entities, the scale of the comparison and the aspect on which the entities are being compared. Our methodology is based on dependencies obtained by applying a parser to extract a wide range of comparison structures. We evaluated our system for its effectiveness in identifying comparisons and their components. The system achieved a F-score of 0.87 for comparison sentence identification and 0.77-0.81 for identifying its components.
Increased cancer risk in a cohort of 230 patients with hereditary hemochromatosis in comparison to matched control patients with non–iron‐related chronic liver disease

It has been suggested that excess iron may facilitate the occurrence of cancer. Patients with hereditary hemochromatosis (HH) are at high risk of developing liver cancer, and studies of limited series reported a high frequency of nonhepatic cancers. To verify whether patients with HH are at higher risk of liver cancer and other malignancies as compared with patients with non–iron‐related chronic liver disease (CLD), we analyzed the occurrence of neoplasms in 230 patients with HH and 230 with non–iron‐related CLD. The patients were matched by sex, age, duration of follow‐up (±5 years), and severity of liver disease. On enrollment, the following variables were considered: hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, alcohol abuse, smoking, and a family history of cancer (first‐degree relatives). The diagnosis of primary cancers was confirmed by histology. During the follow‐up, hepatocellular carcinoma (HCC) developed in 49 and 29 patients (all cirrhotic patients) with HH and non–iron‐related CLD, respectively, with a relative risk of 1.8 (95% confidence interval [CI] 1.1‐2.9); nonhepatic cancers occurred in 20 and 11 patients, respectively, with a relative risk of 1.8 (95% CI 0.8‐4). Four patients with HH and 1 with non–iron‐related CLD developed 2 different primary cancers during follow‐up. The risk of cancer after adjustment for alcohol abuse, smoking, and family history of cancer was 1.9 (95% CI 1.1‐3.1) in the patients with HH. In conclusion, patients with HH are at high risk of both liver cancer and other malignancies, which should be carefully sought during follow‐up.
Diagnostic cross‐linking of paired cysteine pairs demonstrates homologous structures for two chemoreceptor domains with low sequence identity

Hundreds of bacterial chemoreceptors from many species have periplasmic, ligand‐recognition domains of approximately the same size, but little or no sequence identity. The only structure determined is for the periplasmic domain of chemoreceptor Tar from Salmonella and Escherichia coli. Do sequence‐divergent but similarly sized chemoreceptor periplasmic domains have related structures? We addressed this issue for the periplasmic domain of chemoreceptor TrgE from E. coli, which has a low level of sequence similarity to Tar, by combining homology modeling and diagnostic cross‐linking between pairs of introduced cysteines. A homology model of the TrgE domain was created using the homodimeric, four‐helix bundle structure of the TarS domain from Salmonella. In this model, we chose four pairs of positions at which introduced cysteines would be sufficiently close to form disulfides across each of four different helical interfaces. For each pair we chose a second pair, in which one cysteine of the original pair was shifted by one position around the helix and thus would be less favorably placed for disulfide formation. We created genes coding for proteins containing four such pairs of cysteine pairs and investigated disulfide formation in vivo as well as functional consequences of the substitutions and disulfides between neighboring helices. Results of the experimental tests provided strong support for the accuracy of the model, indicating that the TrgE periplasmic domain is very similar to the TarS domain. Diagnostic cross‐linking of paired pairs of introduced cysteines could be applied generally as a stringent test of homology models.
Onsite QTc Interval Screening for Patients in Methadone Maintenance Treatment

ABSTRACT To improve the electrocardiogram screening process and early detection of patients at high risk for cardiac arrhythmias, the authors created a model in their clinic where they provided an onsite electrocardiogram screening that might be feasible and practical. The authors then performed a retrospective chart review to access the efficacy and feasibility of their new onsite procedure in identifying methadone maintained patients at high risk for cardiac arrhythmias. Records from all patients who are currently or had previously been maintained on methadone in the methadone maintenance program at the Atlanta VA Medical Center between 2002 and 2009 were evaluated. Of the 140 patients treated at the clinic between 2002 and 2009, 85 were excluded from the study because they had been treated as guests (had been in treatment in other clinics but received methadone dosing temporarily from our clinic), were treated in the clinic for less than 6 months, or dropped out of treatment. Thus, 55 patient charts were selected for review. Most patients (95%) received baseline and annual electrocardiogram screening. The average baseline QTc was (417 ± 30) and most recent QTc (442 ± 25). This QTc prolongation from baseline showed statistical significance (P < .0001). Sixty-seven percent of patients had statistically significant QTc prolongation from baseline but was less than 450 ms (mean: 428 ± 16, P = .008). Twenty-seven percent of patients had statistically significant QTc prolongation from baseline of more 450 ms but was less than 500 ms (mean: 460 ± 8, P < .0001). Six percent of patients had statistically significant QTc prolongation from baseline of more 500 ms (mean: 503 ± 1.15, P = .027). Recent cocaine use was the only individual variable that showed statistically significant correlation with QTc prolongation (F = 6.98, P = .01). The authors demonstrated in this study that providing an onsite electrocardiogram screening with a focus on patient education and limiting the referral to specialty care for patients at high risk for cardiac arrhythmias could be practical and feasible.
Regulation of Anguillicola crassus (Nematoda) infrapopulations in their definitive host, the European eel, Anguilla anguilla

SUMMARY The parasitic nematode Anguillicola crassus was recently introduced into populations of the European eel, Anguilla anguilla. We investigated, under experimental conditions, the regulation of A. crassus infrapopulations. We tested the effects of (1) the resource-limited habitat of the parasite and (2) the coexistence of several developmental stages in its niche (the swim-bladder) on the composition of the infrapopulations. The results revealed that the respective effects of these factors differed substantially during the course of the infection. Third-stage larvae (L3s) establishment would not be constrained by the size of the swim-bladder. Their moult to fourth-stage larvae (L4s) would be accelerated as the number of L3s increased. The moulting time of L4s to adults would be reduced by males and would be constrained by the size of the swim-bladder. However, the moult of L4s to adults and their further development would be synchronized with those of the opposite sex. At the time of mating, the number of males and the body weight of adults would depend on the size of the swim-bladder. Soon after the laying of eggs, the developmental constraint on the late L3s would decrease. When adults die, constraints would cease and late larval stages would moult to become adults.
HeLa Cells: Effects of Temperature on the Life Cycle

After a shift in temperature, the population kinetics of HeLa cells does not immediately reach a steady state characteristic of the new temperature. During the transition period the duration of each period of the life cycle (period before DNA synthesis, of DNA synthesis, after DNA synthesis, and the period of mitosis) increases toward its steady-state value. Of the four periods, the period before DNA synthesis reaches its steady-state value fastest. Exponential growth can be maintained only from 33�C through 40�C. The period of mitosis is the most temperature-sensitive period of the life cycle of the cell. At subnormal temperatures (26�C through 31�C) there is an accumulation of cells in mitosis, and mitotic indices as high as 0.44 can be obtained. The duration of mitosis is a function both of the temperature and of the time which the cell has spent at this temperature.
The Effect of Childhood Trauma on Later Psychological Adjustment

This study examined whether adult attachment and cognitive distortion mediate the relationship between childhood trauma and psychological adjustment. The participants were 219 students (40 men and 117 women) enrolled in a university degree. Participants completed the Childhood Trauma Questionnaire, which assessed retrospective accounts of childhood trauma; the Relationships Scales Questionnaire, which measured two dimensions of adult attachment (model-of-self and model-of-other); the Cognitive Distortions Scale, which measured internal attributions and perceptions of controllability; and the Trauma Symptom Inventory, which assessed posttraumatic symptoms and was used in this study to measure psychological adjustment. Results supported the hypothesis that model-of-self and cognitive distortion are related constructs. The influence of model-of-self on psychological adjustment however was only via its effect on cognitive processes. In other words, a negative model-of-self influenced cognitive distortion, which in turn influenced the expression of symptoms in adults reporting a history of childhood trauma. The implications for therapy were considered.
Glucose regulated proteins in cancer progression, Drug resistance and immunotherapy

It has been established that as molecular chaperones, the glucose regulated proteins (GRPs) play an important role in maintaining cellular homeostasis. This conventional concept of GRPs as protein folding chaperones is updated by discoveries that GRPs promote tumor proliferation, metastasis, drug resistance, immunotherapy, which have major clinical implications in the prognosis and treatment of cancer. Further, the localization of GRPs on the cell surface of certain cell types suggests that they serve new functions as cell surface receptors for signaling. These and other new developments on the role of GRP78, GRP94 and GRP170 in cancer progression and therapy are discussed in this review.
Corpectomy: a direct approach to perimedullary arteriovenous fistulas of the anterior cervical spinal cord.

OBJECT In this report, the authors describe five consecutive patients with cervical perimedullary arteriovenous fistulas (AVFs) that were successfully treated using a corpectomy performed via an anterior approach. METHODS Five patients with cervical perimedullary AVF underwent corpectomy via an anterior approach. There were four women and one man who ranged in age from 34 to 62 years (median 55 years). Four patients presented with subarachnoid hemorrhage and one with intramedullary hemorrhage. All five AVFs were located on the anterior surface of the cervical spinal cord and fed by the anterior spinal artery. All patients underwent an anterior approach with 1.5- or two-level corpectomy, opening of the dura mater, and coagulation of the fistula. After dural closure, an iliac bone graft was inserted. Four patients were treated by surgery alone and one patient by embolization and surgery. Postoperative angiography revealed complete disappearance of the AVF in all patients. Neurological status improved in two cases and stabilized in the other three. There were no surgery-related complications. CONCLUSIONS Safe and effective interruption of cervical AVFs can be accomplished by an anterior-approach corpectomy.
Surface heparin treatment of the decellularized porcine heart valve: Effect on tissue calcification.

Tissue calcification is a major cause of failure of bioprosthetic heart valves. Aim of this study was to examine whether surface heparin treatment of the decellularized porcine heart valve reduces tissue calcification. Fresh porcine aortic heart valves were dissected as tissue discs and divided into four groups. Group A: controls without treatment, Group B: decellularization only, Group C: decellularization and glutaraldehyde cross-linking, Group D: decellularization and glutaraldehyde cross-linking followed by surface heparin treatment. After implantation in New Zealand White rabbits for 60 days, the explanted heart valve discs from the different study groups underwent a series of histological examinations as well as determination of calcium content by the methyl thyme phenol blue colorimetric method. Results of the explanted heart valve discs for the Von Kossa staining demonstrated that in Group A the heart valve tissue was the most severely stained with black color, whereas in Group D there was hardly any area that was stained black after implantation indicating the least tissue calcification. Furthermore, the inflammatory cells identified by the Hematoxylin-eosin staining appeared to be the least in Group D. The average tissue calcium content was highest in Group A (0.197 ± 0.115 μmol mg-1 ), modest in Group B (0.113 ± 0.041 μmol mg-1 ), and Group C (0.089 ± 0.049 μmol mg-1 ), and the lowest in Group D (0.019 ± 0.019 μmol mg-1 , p < 0.05). These results suggest that surface heparin treatment tends to reduce tissue calcification of the dellellularized porcine heart valve in a rabbit intramuscular implantation model. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 400-405, 2017.
Comparison of methods for in vitro testing of susceptibility of porcine Mycoplasma species to antimicrobial agents

The MICs of 18 antimicrobial agents used against strains of three porcine Mycoplasma species were determined by a serial broth dilution method. Twenty field strains of M. hyorhinis, ten field strains of M. hyopneumoniae, six field strains of M. flocculare, and the type strains of these species were tested. Twelve field strains and the type strain of M. hyorhinis were also tested by an agar dilution method. Tests were read at various time points. When the broth dilution method was used, the final MIC had to be read 2 days after color changes had stopped. MICs of tetracycline, oxytetracycline, doxycycline, and minocycline were low for the three Mycoplasma species tested. MICs of chlortetracycline were 8 to 16 times higher than MICs of the other tetracyclines. Spiramycin, tylosin, kitasamycin, spectinomycin, tiamulin, lincomycin, and clindamycin were effective against all strains of M. hyorhinis and M. hyopneumoniae. The quinolones were highly effective against M. hyopneumoniae but less effective against M. hyorhinis. The susceptibility patterns for M. hyopneumoniae and M. flocculare were similar.
Nosocomial Outbreak of Infection With Pan–Drug-Resistant Acinetobacter baumannii in a Tertiary Care University Hospital

Objective. TO describe what is, to our knowledge, the first nosocomial outbreak of infection with pan–drug-resistant (including colistin-resistant) Acinetobacter baumannii, to determine the risk factors associated with these types of infections, and to determine their clinical impact. Design. Nested case-control cohort study and a clinical-microbiological study. Setting. A 1,521-bed tertiary care university hospital in Seville, Spain. Patients. Case patients were inpatients who had a pan-drug-resistant A. baumannii isolate recovered from a clinical or surveillance sample obtained at least 48 hours after admission to an intensive care unit (ICU) during the time of the epidemic outbreak. Control patients were patients who were admitted to any of the “boxes” (ie, rooms that partition off a distinct area for a patient's bed and the equipment needed to care for the patient) of an ICU for at least 48 hours during the time of the epidemic outbreak. Results. All the clinical isolates had similar antibiotic susceptibility patterns (ie, they were resistant to all the antibiotics tested, including Colistin), and, on the basis of repetitive extragenic palindromic-polymerase chain reaction, it was determined that all of them were of the same clone. The previous use of quinolones and glycopeptides and an ICU stay were associated with the acquisition of infection or colonization with pan-drug-resistant A. baumannii. To control this outbreak, we implemented the following multicomponent intervention program: the performance of environmental decontamination of the ICUs involved, an environmental survey, a revision of cleaning protocols, active surveillance for colonization with pan-drug-resistant A. baumannii, educational programs for the staff, and the display of posters that illustrate contact isolation measures and antimicrobial use recommendations. Conclusions. We were not able to identify the common source for these cases of infection, but the adopted measures have proven to be effective at controlling the outbreak.
Modulation instability, Cherenkov radiation, and Fermi–Pasta–Ulam recurrence

The work of J.M.S.C. is supported by the Ministerio de Economia y Competitividad under contract FIS2009-09895. The authors acknowledge the support of the Australian Research Council (Discovery Project No. DP110102068). N.A. is a recipient of the Alexander von Humboldt Award.
PLATE FIXATION OF ODONTOID FRACTURES WITHOUT C1–C2 ARTHRODESIS: PRACTICE OF A NOVEL SURGICAL TECHNIQUE FOR STABILIZATION OF ODONTOID FRACTURES, INCLUDING THE OPPORTUNITY TO EXTEND THE FIXATION TO C3

OBJECTIVESurgical treatment of odontoid fractures that do not allow interfragmentary fracture compression involves either posterior atlantoaxial arthrodesis or additional anterior stabilization using a plate construct. The purpose of this study was to determine the clinical and radiographic outcome after anterior plate fixation of odontoid fractures that were not suitable for anterior screw fixation. METHODSWe reviewed the clinical and radiographic records of 9 patients with an average age of 54 years at the time of surgery who had undergone anterior plate fixation of an odontoid fracture. Indications for using a plate construct were odontoid fractures with anterior oblique fracture lines, fractures with comminution or major displacement, and pathological fractures. RESULTSEight patients returned to their preinjury activity level and were satisfied with their treatment. One patient reported chronic pain symptoms and a notable decrease in cervical spine motion. Using the Smiley-Webster Scale to quantify their clinical outcome, we achieved an overall outcome score of 1.6. Bony fusion was achieved in all patients. Reduction or fixation failed in 2 patients. Reoperation for technical failures was not necessary in any of the patients. CONCLUSIONWe had promising results using anterior plate fixation for surgical treatment of odontoid fractures that did not allow interfragmentary fracture compression. Because this method avoids the rigid fixation of the atlantoaxial joint in contrast to techniques of posterior cervical arthrodesis, it seems to be a practical option for the management of fracture types that require additional stabilization of the odontoid.
Isolation, identification and characterization of probiotic Lactobacilli spp. from Tarkhineh.

“Tarkhineh” is a traditional fermented food produced from a mixture of spontaneously fermented butter milk and wheat flour in Iran. Nine samples of Tarkhineh were collected from different rural areas in Kermanshah province, Iran. The isolates were grouped and identified using a combination of phenotypic and genotypic methods including repetitive extragenic palindromic polymerase chain reaction (REP-PCR) fingerprinting, biochemical methods and carbohydrate profiling and then evaluation the probiotic properties of them. According to the results these 54 isolates belonged to Lactobacillus plantarum (19), Lactobacillus fermentum (17), Lactobacillus pentosus (9), Lactobacillus brevis (8) and Lactobacillus diolivorans (1) that profile bonding from rep-PCR showed Lactobacillus plantarum have a high intra-species diversity. Media of pH = 2.0–7.0 and bile salt concentrations of 0.0-0.5% were used as stress conditions. Antibacterial activity of the probiotic Lactobacillus was determined by means of the spot-on-lawn method. In conclusion, our results showed that 3 strains have potential probiotic value that two of them was Lactobacillus fermentum and one of them was Lactobacillus plantarum.
Spectrophotometric evaluation of peroxide penetration into the pulp chamber from whitening strips and gel: An in vitro study

Aim: To investigate pulp chamber penetration of different concentration of hydrogen peroxide. Materials and Methods: Fifty extracted human maxillary central incisor teeth were taken and grouped into five (n = 10). All teeth were cut approximately 3 mm apical to the cemento-enamel junction. Pulp was removed and the pulp chamber filled with acetate buffer. Buccal crown surfaces of teeth in the experimental groups were subjected to whitening strip and paint on whitener gel. Control group teeth were exposed to distilled water. The acetate buffer solution in each tooth was then transferred to a glass test tube after 30 min. Leuco-crystal violet dye and enzyme horse radish peroxidase were added. The optical density of resultant blue color in the tubes was measured by UV-visible spectrophotometer. The values were converted into microgram equivalents of hydrogen peroxide. Results: The results were evaluated statistically using nonparametric Mann–Whitney U test. Whitening strip showed the lowest pulpal peroxide penetration whereas paint on whitener gel showed highest pulpal peroxide penetration. Conclusion: This study demonstrate that peroxide is readily penetrate into the pulp chamber of teeth.
Gastric Carcinoma in Young Adults

Of 720 patients with gastric carcinoma treated over a 6-year period, 37 (5%) were 35 years of age or younger. They differed from older patients in that the usual sex ratio was altered (18 men: 19 women), and in certain histologic features. Poorly differentiated or undifferentiated lesions predominated (34 patients), and the distribution of histologic types was unusual; two thirds each were of the diffuse type (Lauren classification) or signet ring type (World Health Organization classification), and over three quarters were infiltrative (Ming classification). Intestinal metaplasia was absent in the majority of patients, and gastritis was less commonly seen than in older patients. Although most patients had long histories of disease and advanced disease, the TNM stages and the proportion undergoing curative resection (8%) were similar to those seen in older patients. Except for one who has survived 5 years, all patients in this study have died.
Satisfacción de los servicios de salud y su relación con la calidad en los hospitales públicos de Ixmiquilpan, Hgo.

El ofrecer atencion de buena calidad siempre ha sido una meta tanto para los gerentes como para los profesionales de salud los cuales disenan programas y estrategias que estan procurando ofrecer mejor atencion a mas personas. Las estrategias que se han planteado buscan unificar los esfuerzos de las principales instituciones del sistema de salud, con el objeto de desarrollar criterios uniformes. Este esfuerzo actualmente se lleva en un programa disenado para la mejora de la calidad de la atencion medica que recibe la poblacion en el pais.