bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of ATP binding residues of a protein from its primary sequence
Authors: Chauhan Jagat S , Mishra Nitish K , Raghava Gajendra PS 
Published: December 2009

Abstract

Background
One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. The function of many proteins depends on their interaction with small molecules or ligands. ATP is one such important ligand that plays critical role as a coenzyme in the functionality of many proteins. There is a need to develop method for identifying ATP interacting residues in a ATP binding proteins (ABPs), in order to understand mechanism of protein-ligands interaction.

Results
We have compared the amino acid composition of ATP interacting and non-interacting regions of proteins and observed that certain residues are preferred for interaction with ATP. This study describes few models that have been developed for identifying ATP interacting residues in a protein. All these models were trained and tested on 168 non-redundant ABPs chains. First we have developed a Support Vector Machine (SVM) based model using primary sequence of proteins and obtained maximum MCC 0.33 with accuracy of 66.25%. Secondly, another SVM based model was developed using position specific scoring matrix (PSSM) generated by PSI-BLAST. The performance of this model was improved significantly (MCC 0.5) from the previous one, where only the primary sequence of the proteins were used.

Conclusion
This study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence. The evolutionary information is important for the identification of 'ATP interacting residues', as it provides more information compared to the primary sequence. This method will be useful for researchers studying ATP-binding proteins. Based on this study, a web server has been developed for predicting 'ATP interacting residues' in a protein http://www.imtech.res.in/raghava/atpint/.
Diagnostic Usefulness of Fluorescent Cytogenetics in Differentiating Chromophobe Renal Cell Carcinoma From Renal Oncocytoma
Authors: Brunelli Matteo , Delahunt Brett , Gobbo Stefano , Tardanico Regina , Eccher Albino , Bersani Samantha , Cossu-Rocca Paolo , Parolini Claudia , Balzarini Piera , Menestrina Fabio , Cheng Liang , Eble John Nelson , Martignoni Guido 
Published: December 2009

Abstract
We investigated the usefulness of interphase fluorescence in situ hybridization (FISH) analysis to differentiate between 11 chromophobe renal carcinomas and 12 renal oncocytomas, showing different clinical outcomes, when compared with conventional metaphase cytogenetics by karyotyping.
Karyotypically, 3 chromophobe renal cell carcinomas showed losses of chromosomes, 3 were polyploid, 1 was normal, and 4 failed to grow. Of 12 oncocytomas, 5 showed a normal numeric karyotype and 6 additional structural rearrangements. FISH on chromophobe renal cell carcinomas showed a high percentage of cases (10/11 [91%]) with multiple numeric losses among chromosomes 1, 2, 6, 10, and 17; this interphase pattern was observed irrespective of the 3 different metaphase karyotypes. Of 12 oncocytomas, 11 (92%) revealed a normal numeric chromosomal status showing at least 2 chromosomes without aneusomy by interphase FISH.
The study demonstrates that indeed FISH performed on formalin-fixed, paraffin-embedded tissue can provide clinically useful information more reliably than karyotyping of most of these tumors.
Selected Reaction Monitoring–Mass Spectrometric Immunoassay Responsive to Parathyroid Hormone and Related Variants
Authors: Lopez Mary F , Rezai Taha , Sarracino David A , Prakash Amol , Krastins Bryan , Athanas Michael , Singh Ravinder J , Barnidge David R , Oran Paul , Borges Chad , Nelson Randall W 
Published: December 2009

AbstractBackground: Parathyroid hormone (PTH) assays able to distinguish between full-length PTH (PTH1–84) and N-terminally truncated PTH (PTH7–84) are of increasing significance in the accurate diagnosis of endocrine and osteological diseases. We describe the discovery of new N-terminal and C-terminal PTH variants and the development of selected reaction monitoring (SRM)-based immunoassays specifically designed for the detection of full-length PTH [amino acid (aa)1–84] and 2 N-terminal variants, aa7–84 and aa34–84.Methods: Preparation of mass spectrometric immunoassay pipettor tips and MALDI-TOF mass spectrometric analysis were carried out as previously described. We used novel software to develop SRM assays on a triple-quadrupole mass spectrometer. Heavy isotope-labeled versions of target peptides were used as internal standards.Results: Top-down analysis of samples from healthy individuals and renal failure patients revealed numerous PTH variants, including previously unidentified aa28–84, aa48–84, aa34–77, aa37–77, and aa38–77. Quantitative SRM assays were developed for PTH1–84, PTH7–84, and variant aa34–84. Peptides exhibited linear responses (R2 = 0.90–0.99) relative to recombinant human PTH concentration limits of detection for intact PTH of 8 ng/L and limits of quantification of 16–31 ng/L depending on the peptide. Standard error of analysis for all triplicate measurements was 3%–12% for all peptides, with &lt;5% chromatographic drift between replicates. The CVs of integrated areas under the curve for 54 separate measurements of heavy peptides were 5%–9%.Conclusions: Mass spectrometric immunoassays identified new clinical variants of PTH and provided a quantitative assay for these and previously identified forms of PTH.
β-cell development and turnover during prenatal life in humans
Authors: Meier Juris J , Köhler Christina U , Alkhatib Bacel , Sergi Consolato , Junker Theresa , Klein Harald H , Schmidt Wolfgang E , Fritsch Helga 
Published: December 2009

Introductionβ-cell regeneration is an area under active investigation for the future treatment of diabetes, but little is known about the patterns and dynamics of prenatal β-cell development in humans. In particular, the quantitative changes in β-cell mass in the developing pancreas have not been elucidated in detail. We addressed the following questions in prenatal humans: i) what is the timing of β-cell occurrence and islet growth? ii) What are the dynamics of β-cell replication and apoptosis?MethodsPancreatic tissue was obtained from 65 human embryos and foetuses aged between 8 weeks post conception (p.c.) and birth. Sections were stained for insulin, glucagon, Ki67 (proliferation marker), TUNEL (apoptosis marker) and CD31 (blood vessel marker), and morphometric analyses were performed.Resultsβ-cells were detected from gestational week 9 onward, whereas glucagon expression was detected already at week 8. The fractional β-cell area of the pancreas increased in a linear fashion until birth (r=0.60, P<0.001). The first endocrine cells were found within or adjacent to the primitive ductal epithelium. β-cell replication was readily detected in the newly forming islets already starting at week 9 p.c. (average frequency 2.8±0.4%). A small percentage of cells co-expressed insulin and glucagon during the early foetal period. There was a close relationship between the development of endocrine islets and blood vessels during all stages of prenatal pancreas development suggesting a possible interaction between both cell types. The frequency of β-cell apoptosis was relatively high throughout all ages (1.5±0.3%).Conclusionsβ-cell differentiation in humans occurs from week 9 p.c. onward. The first endocrine cells are closely associated with the ductal epithelium suggesting differentiation from precursor cells. High rates of β-cell replication suggest that this mechanism plays an important role in the prenatal expansion of β-cell mass.
Gait Parameters Associated With Responsiveness to Treadmill Training With Body-Weight Support After Stroke: An Exploratory Study
Authors: Mulroy Sara J. , Klassen Tara , Gronley JoAnne K. , Eberly Valerie J. , Brown David A. , Sullivan Katherine J. 
Published: December 2009

Background
Task-specific training programs after stroke improve walking function, but it is not clear which biomechanical parameters of gait are most associated with improved walking speed.

Objective
The purpose of this study was to identify gait parameters associated with improved walking speed after a locomotor training program that included body-weight–supported treadmill training (BWSTT).

Design
A prospective, between-subjects design was used.

Methods
Fifteen people, ranging from approximately 9 months to 5 years after stroke, completed 1 of 3 different 6-week training regimens. These regimens consisted of 12 sessions of BWSTT alternated with 12 sessions of: lower-extremity resistive cycling; lower-extremity progressive, resistive strengthening; or a sham condition of arm ergometry. Gait analysis was conducted before and after the 6-week intervention program. Kinematics, kinetics, and electromyographic (EMG) activity were recorded from the hemiparetic lower extremity while participants walked at a self-selected pace. Changes in gait parameters were compared in participants who showed an increase in self-selected walking speed of greater than 0.08 m/s (high-response group) and in those with less improvement (low-response group).

Results
Compared with participants in the low-response group, those in the high-response group displayed greater increases in terminal stance hip extension angle and hip flexion power (product of net joint moment and angular velocity) after the intervention. The intensity of soleus muscle EMG activity during walking also was significantly higher in participants in the high-response group after the intervention.

Limitations
Only sagittal-plane parameters were assessed, and the sample size was small.

Conclusions
Task-specific locomotor training alternated with strength training resulted in kinematic, kinetic, and muscle activation adaptations that were strongly associated with improved walking speed. Changes in both hip and ankle biomechanics during late stance were associated with greater increases in gait speed.
Saline infusion sonohysterography – an effective tool for evaluation of the endometrial cavity in women with abnormal uterine bleeding
Authors: MATHEW MARIAM , GOWRI VAIDYANATHAN , RIZVI SYED GAUHAR 
Published: December 2009

AbstractWe evaluated the diagnostic accuracy of saline infusion sonohysterography (SISH) over transvaginal sonography (TVS) for the detection of intrauterine abnormalities using hysteroscopy as the gold standard in a retrospective study of 70 women mostly presenting with abnormal uterine bleeding. TVS was normal in 32 women, while in the others polyps or fibroids projecting into the cavity (n = 19) or a thick endometrium (n = 19) were suspected. On performing SISH the uterine cavity was found to be normal in 29 women, while 35 had suspected polyps/fibroids and 6 had other abnormalities. Hysteroscopy proved to be normal in 28 women, 35 had polyps/fibroids and 7 had other abnormalities. The sensitivity, specificity, positive and negative predictive values for TVS were 72.4%, 100%, 100% and 74%, respectively, while for SISH the corresponding figures were 91.4%, 92.6%, 89.3% and 94.1%. SISH is a simple, minimally invasive and cost‐effective investigative tool enhancing the diagnostic accuracy of TVS and can be an effective screening test prior to hysteroscopy.
Does low molecular weight heparin shorten term labor?
Authors: EKMAN‐ORDEBERG GUNVOR , ÅKERUD ANNA , DUBICKE AURELIJA , MALMSTRÖM ANDERS , HELLGREN MARGARETA 
Published: December 2009

AbstractDalteparin, a low molecular weight heparin (LMWH), is given to pregnant women with thrombotic disorders. Clinical observations together with the documented changes of heparan sulfate proteoglycans in normal and protracted labor fostered the idea that LMWH shortens delivery time. Labor time was retrospectively determined among nulliparous pregnant women treated with dalteparin because of previous venous thromboembolism (VTE), thrombophilia or acute VTE during current pregnancy. Their labor time was compared to matched untreated controls. The proportion of instrumental deliveries and neonatal outcome was also compared. The dalteparin‐treated group showed a significantly (30%) shorter labor time compared to matched controls. Total instrumental deliveries were the same in the two groups but operative intervention due to protracted labor was significantly less common in dalteparin‐treated women. There was no difference in neonatal outcome. Dalteparin most likely shortens parturition time and may decrease the number of operative interventions due to protracted labor.
Laparoscopic versus ultraminilaparotomic myomectomy for the treatment of large uterine myomas
Authors: CIAVATTINI ANDREA , TSIROGLOU DIMITRIOS , TRANQUILLI ANDREA LUIGI , LITTA PIETRO 
Published: December 2009

AbstractWe compared short‐term surgical outcomes of laparoscopic and ultraminilaparotomic procedures for the treatment of large uterine myomas in a retrospective matched‐control study (Canadian Task Force classification II‐2) of 32 women with large myomas who underwent laparoscopic myomectomy and 32 women who had ultraminilaparotomic myomectomy (≤4 cm incision). Myomectomies were successfully performed for all women in both groups, but time to discharge was significantly lower after laparoscopic than after ultraminilaparotomic myomectomy (p = 0.01). Laparoscopic myomectomy seems to be the preferable approach for the treatment of large myomas of ≥5 cm, providing a more rapid recovery compared to the ultraminilaparotomic approach. Ultraminilaparotomy may be a valid alternative in case of laparoconversion instead of the classic laparotomy approach.
Downregulated CD44 and hyaluronan expression in vulvar intraepithelial neoplasia and squamous cell carcinomas
Authors: HÄMÄLÄINEN KIRSI , KOSMA VELI‐MATTI , ELORANTA MARJA‐LIISA , TAMMI RAIJA , TAMMI MARKKU , LEPPÄNEN MARJO , LEPPÄNEN MERJA , HEINONEN SEPPO , ANTTILA MAARIT 
Published: December 2009

AbstractObjective. To investigate the expression of CD44 and hyaluronan in vulvar squamous cell carcinomas, vulvar intraepithelial neoplasia (VIN) and lichen sclerosus (LS) cases. Design. Retrospective study. Setting. Kuopio University Hospital in Finland. Samples and methods. A total of 18 vulvar squamous cell carcinomas, 22 VIN and 14 LS cases were studied by immunohistochemistry and histochemistry. Co‐localization of these markers was also studied by dual fluorescence staining. Main outcome measures. Expression and cellular localization of CD44 and hyaluronan. Results. In the normal squamous cell epithelium and in most LS samples, CD44 and hyaluronan were expressed homogeneously along plasma membranes with extensive co‐localization. In carcinomas and VIN, both CD44 and hyaluronan were mostly irregular and without co‐localization. In most VIN samples, CD44 was membranous, while hyaluronan was intracellular in 45% of the cases. CD44 showed both plasma membrane and intracellular localization in 39% of the carcinomas and in 94% of the cases hyaluronan was located only intracellularly. In LS, stromal hyaluronan staining was stronger than in carcinomas (p = 0.01). CD44 and hyaluronan staining was not associated with the grade of VIN, while there was good differentiation in carcinomas associated with preserved membranous CD44 (p = 0.012). Hyaluronan was not associated with the grade or stage of cancer. Conclusions. Differences in hyaluronan and CD44 expression in VIN and squamous cell carcinomas compared to normal epithelium suggest that they have a role in vulvar malignancy.
Young girls with malignant ovarian germ cell tumors can undergo normal menarche and menstruation after fertility‐preserving surgery and adjuvant chemotherapy
Authors: YOO SEUNG‐CHUL , KIM WOO YOUNG , YOON JONG‐HYUCK , CHANG SUK‐JOON , CHANG KI‐HONG , RYU HEE‐SUG 
Published: December 2009

AbstractObjective. To evaluate the long‐term outcome and ovarian function in premenarchal and adolescent patients with malignant ovarian germ cell tumors after fertility‐preserving surgery and adjuvant chemotherapy. Design. Retrospective review of medical records. Setting. Ajou University Hospital, a tertiary care hospital in South Korea. Population. Forty‐five patients with malignant ovarian germ cell tumors. Methods. A retrospective analysis of patients with malignant ovarian germ cell tumors was conducted and a statistical analysis was performed. Main outcome measures. There were 9 premenarchal and 16 adolescent patients; the median ages at diagnosis were 7 and 18 years, respectively. All patients were treated with fertility‐preserving surgery. Seventeen of the patients received adjuvant chemotherapy with bleomycin, etoposide, and cisplatin (68.0%). There were no disease recurrences or deaths. Of the nine premenarchal patients, eight (88.9%) subsequently had normal menarche. Among the 16 adolescent patients, 15 (93.8%) resumed normal menstruation and 1 had premature ovarian failure. Conclusion. Premenarchal and adolescent patients with malignant ovarian germ cell tumors have excellent survival with fertility‐preserving surgery and adjuvant chemotherapy. The majority of these patients can have normal menarche and menstruation.
Radical excision of rectovaginal endometriosis results in high rate of pain relief – results of a long‐term follow‐up study
Authors: TARJANNE SATU , SJÖBERG JARI , HEIKINHEIMO OSKARI 
Published: December 2009

AbstractObjective. To evaluate the long‐term results of radical excision for rectovaginal endometriosis (RVE) with special emphasis on current symptoms and risk factors as regards recurrence. Methods. A total of 116 patients operated upon because of RVE were offered a clinical follow‐up evaluation visit; 60 (52%) consented. The time (mean ± SD) from the index surgery to the follow‐up visit was 4.0 ± 0.5 years. Main outcome measures. Daily symptoms using a visual analogue scale for 30 consecutive days prior to clinical assessment; the amount of uterine bleeding was also assessed. Endometriosis recurrence was evaluated via clinical and ultrasonographic examination. Results. The symptom sum scores (maximum 300) were low with median scores (range) of 3 (0–32) for dysmenorrhea and 9 (0–72) for pelvic pain. Evidence of RVE recurrence was found or suspected in 29 (48%) of the 60 women assessed. Clinical recurrence was not associated with pain symptoms. In univariable analysis, amenorrhea at the time of clinical assessment was associated with a lower risk of recurrence (odds ratio; OR 0.13; 95% CI (confidence interval) 0.02–0.65, p = 0.01); the effect of bowel resection was not significant (OR 0.37: 95% CI 0.13–1.07, p = 0.07). In multivariable analysis, the protective effect of bowel resection on recurrence was significant (OR 0.23; 95% CI 0.06–0.89, p = 0.03). Conclusions. Radical surgery may result in long‐term pain relief in cases of RVE. Bowel resection is associated with a lower risk of RVE recurrence. Therapy that induces amenorrhea may be effective in preventing recurrence following surgical treatment of RVE.
Venous thromboembolism in pregnancy: prophylaxis and treatment with low molecular weight heparin
Authors: ANDERSEN ANITA SYLVEST , BERTHELSEN JØRGEN G. , BERGHOLT THOMAS 
Published: December 2009

AbstractObjective. To evaluate the safety of individually dosed low molecular weight heparin (LMWH) for prophylaxis and treatment of thromboembolic complications in pregnancy. Design. Cohort study with a chronologic register‐based control group. Setting. Department of Obstetrics and Gynecology, Hillerød Hospital, Denmark. Population. All 166 women treated with LMWH in pregnancy between 1 January 2001 and 31 December 2005. Methods. Women treated with LMWH in pregnancy were identified and individual case records reviewed retrospectively. General data on the LMWH‐treated women were compared to the 18,020 untreated pregnancies within the same period and with 306 matched controls as regards to postpartum hemorrhage (PPH). Main outcome measures. Side effects of treatment, thromboembolic manifestations, postpartum bleeding and obstetric outcome. Results. There were no thromboembolic events during therapy, few side effects of treatment and no osteoporotic fractures or episodes of heparin‐induced thrombocytopenia. The 166 pregnancies resulted in 159 live infants. There was a significantly higher risk of preterm delivery (13% vs. 6%) and intrauterine growth restriction (4.4% vs. 3.5%). Delivery by cesarean section was more common in these high‐risk LMWH‐treated pregnancies (33.1%) than in untreated pregnancies (19.2%). In the LMWH‐group, the occurrence of PPH was 7.2% compared with 8.8% in the matched untreated control group (p = 0.675). None of the events in the LMWH group were serious and all 166 women were in good health at discharge. Conclusions. Individually dosed LMWH is well tolerated and safe for prophylaxis and treatment of thromboembolic complications during pregnancy, delivery and the postpartum period.
Cervical tissue changes in women with miscarriage: A morphological and biochemical investigation
Authors: RADULOVIC NINA VUKAS , EKERHOVD ERLING , ABRAHAMSSON GUN , NORSTRÖM ANDERS 
Published: December 2009

AbstractObjective. To evaluate morphological and inflammatory events in the uterine cervix in first trimester miscarriages. Design. Experimental study. Setting. Sahlgrenska University Hospital, Gothenburg, Sweden. Population. Nulliparous women with first trimester symptomatic (n = 7) or silent (n = 11) miscarriage scheduled for surgical evacuation and nulliparous women scheduled for surgical termination of first trimester pregnancies (control group n = 11). Methods. Before evacuation, biopsies were obtained from the cervix. The specimens were either fixed in glutaraldehyde for electron microscopy or snap‐frozen in liquid nitrogen and stored at –70°C until analyses of interleukin‐8 (IL‐8) and matrix metalloproteinases (MMPs). Main outcome measures. Ultrastructure of cervical tissue, cervical tissue levels of IL‐8, immunohistochemistry of MMP‐1, MMP‐8, MMP‐9 and IL‐8. Results. The organization of the cervical collagen framework was deranged, the fibroblasts were reactive and the number of activated mast cells appeared to be increased in specimens from women with miscarriage compared with controls. IL‐8 was significantly increased in women with miscarriage. Immunohistochemistry of MMP‐1 and MMP‐8 did not demonstrate any significant difference between the groups. MMP‐9 was significantly lower in specimens from women with symptomatic miscarriage compared to women with silent miscarriage and women in the control group. Conclusions. An inflammatory‐like response takes place in the cervix both in women with symptomatic and silent miscarriage. The intensity of the inflammatory response seems to be similar in the two groups. Therefore, inadequate cervical remodeling does not seem to be the reason why some miscarriages remain silent.