bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using credibility intervals instead of hypothesis tests in SAGE analysis
Authors: Vêncio Ricardo Z.N. , Brentani Helena , Pereira Carlos A.B. 
Published: December 2003

Abstract
Motivation: Statistical methods usually used to perform Serial Analysis of Gene Expression (SAGE) analysis are based on hypothesis testing. They answer the biologist's question: ‘what are the genes with differential expression greater than r with P-value smaller than P?’. Another useful and not yet explored question is: ‘what is the uncertainty in differential expression ratio of a gene?’.
Results: We have used Bayesian model for SAGE differential gene expression ratios as a more informative alternative to hypothesis tests since it provides credibility intervals.
Availability: The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site.
Supplementary information: http://www.ime.usp.br/~rvencio/SAGEci/
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites
Authors: Fariselli Piero , Finocchiaro Giacomo , Casadio Rita 
Published: December 2003

Abstract
Summary: SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting signals and predicts their cleavage sites. The accuracy in cross-validation is similar to that of other available programs: the rate of false positives is 4 and 6%, for prokaryotes and eukaryotes respectively and that of false negatives is 3% in both cases. When a set of 409 prokaryotic lipoproteins is predicted, SPEPlip predicts 97% of the chains in the signal peptide class. However, by integrating SPEPlip with a regular expression search utility based on the PROSITE pattern, we can successfully discriminate signal peptide-containing chains from lipoproteins. We propose the method for detecting and discriminating signal peptides containing chains and lipoproteins.
Availability: It can be accessed through the web page at http://gpcr.biocomp.unibo.it/predictors/
ModLoop: automated modeling of loops in protein structures
Authors: Fiser András , Sali Andrej 
Published: December 2003

Abstract
Summary: ModLoop is a web server for automated modeling of loops in protein structures. The input is the atomic coordinates of the protein structure in the Protein Data Bank format, and the specification of the starting and ending residues of one or more segments to be modeled, containing no more than 20 residues in total. The output is the coordinates of the non-hydrogen atoms in the modeled segments. A user provides the input to the server via a simple web interface, and receives the output by e-mail. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures. For a rapid response, ModLoop runs on a cluster of Linux PC computers.
Availability: The server is freely accessible to academic users at http://salilab.org/modloop
Purinergic receptor expression in the regenerating epidermis in a rat model of normal and delayed wound healing
Authors: Greig Aina V. H. , James Stuart E. , McGrouther D Angus , Terenghi Giorgio , Burnstock Geoffrey 
Published: December 2003

Abstract:  This study investigated changes in the protein expression of purinergic receptors in the regenerating rat epidermis during normal wound healing, in denervated wounds, and in denervated wounds treated with nerve growth factor (NGF), where wound healing rates are normalized. Excisional wounds were placed within denervated, pedicled, oblique, groin skin flaps, and in the contralateral abdomen to act as a control site. Six rats had NGF‐treated wounds and six had untreated wounds. Tissue was harvested at day four after wounding. The re‐epithelializing wound edges were analyzed immunohistochemically for P2X5, P2X7, P2Y1 and P2Y2 receptors, and immunostaining of keratinocytes was quantified using optical densitometry.In normal rat epidermis, P2Y1 and P2Y2 receptors were found in the basal layer where keratinocytes proliferate; P2X5 receptors were associated with proliferating and differentiating epidermal keratinocytes in basal and suprabasal layers; P2X7 receptors were associated with terminally differentiated keratinocytes in the stratum corneum. In the regenerating epidermis of denervated wounds, P2Y1 receptor protein expression was significantly increased in keratinocytes (P < 0.001) but P2Y2 receptor protein expression was significantly decreased (P < 0.001). Conversely, NGF treatment of denervated wounds, reduced expression of P2Y1 receptors (P < 0.001) in keratinocytes but enhanced expression of the P2Y2 receptors (P < 0.01) compared with untreated denervated wounds. In innervated wounds, NGF treatment enhanced P2X5 (P < 0.001) and P2Y1 receptor protein (P < 0.001) expression in keratinocytes. P2X7 receptors were absent in all experimental wound healing preparations. P2X5, P2X7, P2Y1 and P2Y2 receptor protein expression in the regenerating epidermis was altered both during wound healing and also by NGF treatment. Possible roles for purinergic signalling and its relation to NGF in wound healing are discussed.
Delivering an effective outpatient service in gynaecology: an assessment of patient preference
Authors: Marsh Fiona , Taylor Lydia , Kremer Christian , Black Jean , Duffy Sean 
Published: December 2003

ABSTRACTObjectives  To assess whether patients would prefer to undergo outpatient or day‐case hysteroscopy for the investigation of abnormal uterine bleeding.Design  An anonymous questionnaire.Setting  A general gynaecology clinic in a large UK teaching hospital.Subjects  250 consecutive patients attending the gynaecology clinic.Main outcome measures  These were patient preference for either outpatient or day‐case hysteroscopy, and the reasons for the decisions.Results  The questionnaire was completed by189 patients (76% response rate). Of these 52% chose outpatient hysteroscopy, 26% chose day‐case hysteroscopy, 17% wanted to let the doctor decide and 5% needed more information. We found that women in employment and those who had previously undergone review were significantly more likely to opt for outpatient hysteroscopy. The most common reason for preferring outpatient hysteroscopy was that the entire process was quick, whereas the main reason for NOT favouring it was the potential for discomfort. The main appeal of day‐case hysteroscopy for patients was that no pain would be felt during the procedure; the most common reason for disliking day‐case hysteroscopy was the possible wait for up to 3 hours in the day‐case unit before hysteroscopy was performed.Conclusions  When given the choice, women prefer to undergo outpatient rather than daycase hysteroscopy for the investigation of abnormal uterine bleeding. From the patient's perspective, the most common reasons for preferring outpatient hysteroscopy are (in order of priority): the speed of the entire process; the uninterrupted sequence of counselling, investigation and information regarding results, and the shorter wait in hospital before the hysteroscopy is performed.
A case–control study comparing 3.6‐mm and 3.1‐mm flexible hysteroscopes
Authors: Marsh Fiona , Jackson Tracy , Duffy Sean 
Published: December 2003

ABSTRACTObjective  To determine whether a 3.1‐mm diameter flexible hysteroscope causes less patient discomfort and requirement for cervical dilatation than a 3.6‐mm hysteroscope.Setting  The outpatient hysteroscopy clinic of a large teaching hospital in the UK.Participants  159 women with abnormal uterine bleeding who required an outpatient hysteroscopy.Design and intervention  A cohort of patients undergoing hysteroscopy with a 3.6‐mm hysteroscope was matched for age, parity and menopausal status with a cohort of patients undergoing hysteroscopy with a 3.1‐mm hysteroscope.Main outcome measures  Pain scores using a 10‐cm visual analogue scale, and women's description of pain using a Likert‐scale question.Results  Significantly more postmenopausal women undergoing a 3.6‐mm required dilatation of the cervical canal compared with those undergoing a 3.1‐mm hysteroscopy (P = 0.02). In both the premenopausal and postmenopausal groups significantly more women undergoing a 3.1‐mm hysteroscopy had a pain score of zero compared with those undergoing a 3.6‐mm hysteroscopy. In the postmenopausal cohort significantly fewer women in the 3.1‐mm group (31% compared with 51% in the 3.6‐mm group) had pain scores of more than three (P = 0.007). There were also significantly more postmenopausal women in the 3.1‐mm group (64% compared with 23% in the 3.6‐mm group) who described either mild pain or no pain whatsoever (P = 0.0003).Conclusion  Decreasing the diameter of the device used in flexible hysteroscopy from 3.6 mm to 3.1 mm results in a significant reduction in pain and discomfort for both premenopausal and postmenopausal women and significantly reduces the requirement for cervical dilatation in postmenopausal women.
Evaluation of laparoscopic management and clinical outcome in women with premature ovarian failure
Authors: Hirota Yutaka , Ohara Satoshi , Nishizawa Haruki , Tada Shin , Udagawa Yasuhiro 
Published: December 2003

ABSTRACTObjective  To analyse the results of laparoscopic ovarian biopsy and the laparoscopically observed morphological features of the ovary in premature ovarian failure (POF), in relation to clinical outcome, and to construct an appropriate guideline for clinical management utilizing laparoscopy.Design  A retrospective study of patient records.Setting  Fujita Health University Hospital.Subjects  19 women with POF, treated between 1991 and 2000.Main outcome measures  The ovaries from 12 patients who underwent laparoscopy were classified, according to morphological features, as sclerotic, atrophic or hypoplastic. The detection rate for a primordial follicle was assessed for each ovarian type, and the correlation between morphological features and patient clinical outcome was investigated.Results  Induction of ovulation was successful in eight of 19 patients (42.1%). Among the 12 patients who underwent laparoscopy, ovulation induction was successful in four, but not in the remaining eight. The rate of detection of a primordial follicle was 50.0% for the four women with successful ovulation induction and 14.2% in the eight other women. With regard to ovarian type, primordial follicles were detected only in sclerotic ovaries. It was shown that cyclic therapy with estrogen and progesterone (CTEP) had appreciably favourable effects, and then the combined therapy with CTEP‐primed gonadotrophin‐releasing hormone (GnRH) agonist and human menopausal gonadotrophin–human chorionic gonadotrophin (hMG–hCG) was a reasonable therapeutic method.Conclusions  There was a clear relation between the rate of detection of primordial follicles and the morphological features of the ovaries. Therefore, laparoscopy should be done an early stage to determine the type of ovary. Furthermore, in establishing whether or not there is a primordial follicle in the ovary, laparoscopy seems to have an important role in the planning of treatment.
Clinical experiences with laparoscopically assisted vaginal hysterectomy in patients who are candidates for abdominal hysterectomy
Authors: Berker Bulent , Dokmeci Fulya 
Published: December 2003

ABSTRACTObjective  To report our 3‐year experience with laparoscopically assisted vaginal hysterectomy (LAVH) in patients who were candidates for abdominal hysterectomy.Design  Between 1997 and 2000, 50 LAVH procedures were done by the authors. All the patients underwent LAVH because of the contraindications to the vaginal route. A 10‐mm infraumbilical trocar, and two 5‐mm trocars, one for each lower quadrant, were placed in all patients. An initial careful inspection of both ureters was carried out but no dissection of ureters was performed, in order to reduce operative time and minimize the risk of bleeding or ureteral vascular compromise. After the dissection of the broad, round and infundibulopelvic ligaments, the bladder was displaced inferiorly with blunt and sharp dissections. The remainder of the surgery was done vaginally, following the entrance to anterior and posterior vaginal fornices.Results  The average operating time was 87 min with a range of 64–96 min. LAVH was not converted to an abdominal procedure in any patient. There were no intraoperative or postoperative complications. The mean uterine weight was 260 ± 45 g and the mean blood loss was 350 mL. The patients remained in the hospital for a mean of 2.5 ± 1 days.Conclusions  We believe that LAVH is not a substitute for vaginal hysterectomy; however LAVH should be a surgical option at all centres, to be used when the indications are appropriate, especially when vaginal hysterectomy is not possible.
Laparoscopic removal of dysgenetic gonads containing a giant seminoma, in an adult patient with testicular feminization syndrome
Authors: Atabekoglu Cem S. , Berker Bulent , Dunder Ilkkan 
Published: December 2003

ABSTRACTObjective  To report the case of an adult woman who had testicular feminization syndrome and developed a giant manifest seminoma in an undescended intrapelvic gonad.Methods  The clinical records of the patient were reviewed.Results  With the diagnosis of a suspicious adnexal mass, laparoscopy was performed in a patient with testicular feminization syndrome and revealed a right gonadal tumour, 10 × 8 cm in size. The gonads were then removed by laparoscopic surgery. Histopathological examination revealed a seminoma in the right gonad. Postoperatively, tumour markers were normal, and abdominal and pelvic computerized tomographic scans and chest radiographs were negative for possible metastatic disease. The patient made an uneventful postoperative recovery and was discharged on postoperative day 2. No adjuvant radiation therapy was given.Conclusion  Although the possibility of a malignant gonad is one of the major concerns associated with a large pelvic mass in adult patients with testicular feminization, we believe that a laparoscopic approach provides a favourable alternative to an open surgical procedure.
Should endometrial biopsy be a routine investigation for recurrent early‐pregnancy loss?
Authors: Badawy Ahmed M. , El‐Gharib Mohamed E. , Zalata Khalid 
Published: December 2003

ABSTRACTObjective  We are investigating the role of endometrial histologic pattern in patients with recurrent abortions.Study methods  The study comprised 123 women who suffered recurrent abortions. All women were scheduled for hysteroscopy in the periovulatory period in addition to the other routine investigations of recurrent abortion. During hysteroscopic evaluation of the cavity, all suspicious lesions were biopsied and subjected to histopathological examination.Results  Seventy‐one women (57.7%) demonstrated normal cavity. Endometrial polyps were found in 12 women (8.9%) and submucous myomas were verified in eight women (6.5%). Intrauterine adhesions were found in 14 women (11.4%). Different congenital anomalies of the uterus were demonstrated in 18 women (14.6%): arcuate uterus (2.4%), bicornuate uterus (2.4%), incomplete uterus (6.6.%) and complete septum (3.2%). Tuberculous endometritis was demonstrated in two cases.Conclusion  It seems that hysteroscopy and endometrial histology give valuable information in patients with recurrent abortion.
Richter's hernia as an unusual complication of laparoscopic sterilization: a case report and review
Authors: Sharma B. , Greenwood P. , Pereira J. , Kumar V. 
Published: December 2003

ABSTRACTUmbilical port site hernia, with minor procedures like laparoscopic sterilization, especially with port of 10 mm or less are very rare. Those involving bowel mainly occur as Richter's hernia, which may be very difficult to diagnose as only a part of bowel wall is involved and the rest of the bowel might be functioning. Therefore the bowel sounds may persist. It is a serious complication as it may cause bowel obstruction, incarceration, necrosis and perforation resulting in peritonitis. Open surgery with reduction of the hernia is the usual mode of treatment, if the bowel is viable, whereas resection is needed if the bowel wall is not viable. High index of suspicion in these cases can lead to early diagnosis, and thus delaying the above life threatening complications.
Haemodynamic, biochemical and haematological changes during hysteroscopic myomectomy
Authors: Darwish Atef M. , Zareh Hassan Zein E. A. 
Published: December 2003

ABSTRACTObjective  To record circulatory volume changes, hyponatraemia, decrease in plasma osmotic pressure, changes in blood picture and coagulation profile in correlation with the size of myoma during hysteroscopic myomectomy.Design  A cross‐sectional prospective comparative study.Setting   Gynaecologic Endoscopy Unit, Assiut University Hospital, Assiut, Egypt.Subjects   Fifty patients undergoing hysteroscopic myomectomy where a balanced general anaesthetic technique was used.Interventions   Patients were divided into two groups according to the size of the submucous myoma. Group A included 25 patients having small submucous myomas (3 cm or less). Group B included those having larger myomas (more than 3 cm). Hysteroscopic myomectomy was done using glycine 1.5% as an irrigating solution for all cases. Haemodynamic measurements included pulse, mean arterial blood pressure and central venous pressure (CVP). Cardiodynamic measurements using non‐invasive thoracic electrical bioimpedence (TEB) included cardiac output (CO), cardiac index (CI), stroke volume (SV), stroke index (SI), end diastolic volume (EDV), end diastolic index (EDI), ejection fraction (EF), peak flow (PF), peak flow index (PFI) and systemic vascular resistance (SVR), arterial blood gases (PaO2, PaCO2), oxygen saturation by pulse oximeter and end tidal CO2 by capnogram. Serum sodium and potassium concentration, blood osmolarity, prothrombin time (PT), prothrombin concentration (PC), partial thromboplastine time (PTT), haemoglobin concentration (HB), haematocrite value (HCT) and platelet count (PLT) were also measured. Absorbed fluid volume and intrauterine pressure (IUP) were also measured.Main outcome measures   Changes in haemodynamics, caerdiodynamics, blood gases and haematological measurements as measured preoperatively and every 15 min for 75 min.Results   The trial showed statistically significant variations regarding haematological and biochemical variables, but it was not associated with clinical signs of hyponatraemia. No signs of cardiac overload or cerebral confusion in both groups. Group B was associated with significant hyponatraemia, increased CVP, hypo‐osmolarity, increased PT and PTT, and increased most of the cardiodynamic parameters.Conclusions  Hysteroscopic myomectomy, despite being the most risky hysteroscopic procedure, can be safely performed in most cases following the safety precautions. Intraoperative fluid absorption, especially with large myomas, is the trigger of some systemic changes. The procedure should be performed by an experienced hysteroscopist using a quick technique with the least possible glycine volume and minimal intrauterine pressure to achieve the goal of a safe out‐patient minimal access surgery.
The analgesic efficacy of intraperitoneal local anaesthetic instillation after laparoscopic gynaecological procedures
Authors: Kayacan Nurten , Arici Gülbin , Karsli Bilge , Zorlu Gürkan , Erman Meliha 
Published: December 2003

ABSTRACTObjective  Patients undergoing laparoscopic procedures may experience postoperative pain. We evaluated the effectiveness of intraperitoneal local anaesthetic instillation after laparoscopic gynaecological procedures.Design  Randomized, double‐blinded, placebo‐controlled trial.Methods  Patients were randomly assigned to one of three groups of 20 patients each. Those in group A received ropivacaine, 20 ml 0.75%, and those in group B received bupivacaine, 20 ml 0.5% intraperitoneally. Those in group C (the control group) received 20 ml 0.9% saline. Pain was assessed, using a visual analogue scale (VAS) and a verbal rating scale (VRS), at 30 min, 60 min, 2 h and 4 h after surgery. Total analgesic consumption and the time to first need for analgesia were also noted.Results  VAS and VRS pain scores were significantly lower in the ropivacaine and bupivacaine groups compared with the placebo group. Patients in group A (ropivacaine) experienced less pain than those in group B (bupivacaine) for all measurements. The time to first need for analgesia was significantly later for the ropivacaine and bupivacaine groups compared with the placebo group. The total analgesic consumption was also significantly lower in those groups than in the placebo group.Conclusion  The results indicated that both ropivacaine and bupivacaine were effective at preventing pain and the need for postoperative analgesic when intraperitoneally instilled. However, ropivacaine is the better choice because of its higher efficacy.
Laparoscopic appendicectomy: an important skill for the gynaecologist
Authors: Calandra Claude , Barabash Ian D. 
Published: December 2003

ABSTRACTObjective  To demonstrate that laparoscopy is an important skill for gynaecologists to acquire. Laparoscopy is now one of the most commonly performed gynaecological procedures, commonly as an investigative tool for acute or chronic pelvic pain. In Australia, thousands of these procedures are performed each year.Methods  We outline here the main authors’ experience and teaching of his trainees, outlining the technique for the performance of this surgery, in three separate clinical entities.Conclusion  The performance of laparoscopic appendicectomy is an important facet of gynaecological training and can be performed by all gynaecologists with basic laparoscopic training.
Audit of laparoscopic surgery for tubal pregnancy in a district general hospital
Authors: Ali N. S. , Arthur P. , Prashar S. 
Published: December 2003

ABSTRACTObjective  To measure the proportion of tubal pregnancies managed laparoscopically and those suitable for laparoscopic surgery based on departmental guidelines in a district general hospital in the northwest of England.Design  A retrospective audit of the surgical management of tubal pregnancies over a 12‐month period.Setting   A district general hospital.Participants   All women operated on for tubal pregnancy in Sharoe Green Hospital between 1 January 2001 and 31 December 2001.Methods   Cases of tubal pregnancy requiring surgery during 2001 were identified from the computerized theatre log. The case notes of these women were reviewed and assessed as to whether they were managed appropriately by laparotomy and laparoscopic surgery.Audit standard   All cases (100%) to be managed appropriately with laparoscopic surgery in accordance with Royal College of Obstetricians and Gynaecologists (RCOG) guidelines.Results   Fifty‐two possible cases were identified. Five were not tubal pregnancies upon review of the notes and therefore excluded. Nine case notes could not be traced by the audit department. The remaining 38 cases of tubal pregnancy were reviewed. A total of 18% of cases underwent appropriate laparotomy and 82% were deemed suitable for operative laparoscopy. Only 39% of tubal pregnancies deemed suitable were managed by appropriately by laparoscopic surgery.Conclusion   The majority of cases of tubal pregnancy were not managed appropriately with laparoscopic surgery in Sharoe Green Hospital. The proportion of tubal pregnancies suitable for laparoscopic surgery in a district general hospital is approximately 82%.