Application of laparoscopic surgery in gallbladder carcinoma

Gallbladder carcinoma (GC) is a rare type of cancer of the digestive system, with an incidence that varies by region. Surgery plays a primary role in the comprehensive treatment of GC and is the only known cure. Compared with traditional open surgery, laparoscopic surgery has the advantages of convenient operation and magnified field of view. Laparoscopic surgery has been successful in many fields, including gastrointestinal medicine and gynecology. The gallbladder was one of the first organs to be treated by laparoscopic surgery, and laparoscopic cholecystectomy has become the gold standard surgical treatment for benign gallbladder diseases. However, the safety and feasibility of laparoscopic surgery for patients with GC remain controversial. Over the past several decades, research has focused on laparoscopic surgery for GC. The disadvantages of laparoscopic surgery include a high incidence of gallbladder perforation, possible port site metastasis, and potential tumor seeding. The advantages of laparoscopic surgery include less intraoperative blood loss, shorter postoperative hospital stay, and fewer complications. Nevertheless, studies have provided contrasting conclusions over time. In general, recent research has tended to support laparoscopic surgery. However, the application of laparoscopic surgery in GC is still in the exploratory stage. Here, we provide an overview of previous studies, with the aim of introducing the application of laparoscopy in GC.

[Analysis of safety and efficacy of laparoscopic surgery for gallbladder carcinoma]

Objective: To examine the efficacy and safety of laparoscopic surgery for gallbladder carcinoma. Methods: The data of 197 gallbladder carcinoma patients admitted at Peking Union Medical College Hospital between January 2012 and September 2022 were analyzed retrospectively. There were 86 males and 111 females,with age of (64.4±9.8)years(range:35 to 89 years). Patients were divided into laparoscopic group(n=53) and open group(n=144) according to different surgical methods. The general information of the two groups were matched by propensity score matching,and the clinical data and prognosis were compared between the two groups. Categorical variables were analyzed using χ2 test or Fisher's exact test,as appropriate. Continuous variables with and without normal distribution were analyzed using t-test and Mann-Whitney U test,respectively. Kaplan-Meier curves with Log-rank test were used to analyze the cumulative survival rates. Results: Forty-eight pairs of patients were matched successfully. There was no difference in general information,cholecystolithiasis,partial hepatectomy,and tumor stage between two groups(all P>0.05). The laparoscopic group had shorter operation time(t=-3.987,P<0.01),less bleeding(Z=-4.862,P<0.01),shorter total(Z=-5.009,P<0.01) and postoperative(Z=-5.412,P<0.01) hospital stay. Seventeen patients had postoperative complications. According to the Clavien-Dindo system,there were 4,11,1,and 1 patient with grade Ⅰ,Ⅱ,Ⅲa,and Ⅲb,respectively. All complications were improved after active treatment. After a median follow-up of 24(36) months(range:3 to 130 months),56 patients(58.3%) survived without tumor,7 patients(7.3%) survived with tumor,and 33 patients(34.4%) died. According to the Kaplan-Meier curves,there was no significant difference between laparoscopic and open groups in disease free(χ2=0.399,P=0.528) and overall(χ2=0.672,P=0.412) survival rates. Conclusions: The laparoscopic surgery is safe and effective in selected patients with gallbladder carcinoma. It can reduce surgical trauma and enhance patient recovery without increasing complication. Its prognosis is similar to that of open surgery.

[Application of enhanced recovery after surgery in perioperative management of patients with gallbladder carcinoma]

Objective: To investigate the efficacy and safety of enhanced recovery after surgery (ERAS) in perioperative management of patients with gallbladder carcinoma. Methods: The data of the patients with gallbladder carcinoma admitted at Peking Union Medical College Hospital between January 2017 and December 2021 were analyzed retrospectively. There were 69 males(42.1%) and 95 females(57.9%),with age of (64.0±10.3) years(range:37 to 89 years). Patients were divided into ERAS group(n=53) and normal group(n=111) according to whether they were treated with ERAS measures during the perioperative period.The basic characteristics of the two groups were matched by propensity score matching,and then the perioperative information was compared between the two groups. Categorical variables were presented as absolute numbers or frequencies. Differences between study groups were analyzed using χ² test, Fisher's exact test, t-test, or Mann-Whitney U test, as appropriate. Results: Each group had 45 patients after propensity score matching with well-balanced basic characteristics. There was no difference in basic characteristics, operation time,bleeding,complication,and hospitalization expenses between two groups(all P>0.05). Compared with the normal group,time of ambulation (M(IQR)) (1(1) day vs. 2(2) days;Z=-3.839,P<0.01),postoperative anal exhaust time (2(1) days vs. 3(1) days;Z=-3.013,P=0.003),feeding time(2(1) days vs. 2(1) days;Z=-3.647,P<0.01),postoperative (5(2) days vs. 7(4) days;Z=-3.984,P<0.01) and total(8(4) days vs. 13(6) days;Z=-3.605,P<0.01) hospitalization time were shorter in ERAS group. Postoperative complications occurred in 12 patients. According to the Clavien-Dindo classification,6,4,and 2 patients were classified as grade Ⅰ,Ⅱ,and Ⅲa,respectively. Conclusion: The ERAS measures is safe and effective for perioperative management of patients with gallbladder carcinoma, enhancing patient recovery and shortening hospitalization time without increasing complication or hospitalization cost.

Risk factors for preoperative carcinogenesis of bile duct cysts in adults

BACKGROUND

Bile duct cyst (BDC) is a rare congenital bile duct malformation. The incidence of bile duct malignancy in BDC patients is markedly higher than that in the general population. However, few studies have been conducted on the risk factors for preoperative carcinogenesis in BDC patients.

AIM

To analyze the risk factors associated with preoperative carcinogenesis in BDC patients.

METHODS

The medical records of BDC patients treated at our hospital between January 2012 and December 2018 were retrospectively reviewed. We constructed a database and compared the characteristics of BDC patients with dysplasia and carcinoma against those with benign cysts. The risk factors for preoperative carcinogenesis were identified using univariate and multivariate analyses.

RESULTS

The cohort comprised 109 BDC patients. Ten patients had preoperative dysplasia or adenocarcinoma. Univariate and multivariate analyses showed that gallbladder wall thickness > 0.3 cm [odds ratio (OR), 6.551; 95% confidence interval (CI), 1.351 to 31.763; P = 0.020] and Todani type IV (OR, 7.675; 95%CI, 1.584 to 37.192; P = 0.011) were independent factors associated with preoperative carcinogenesis.

CONCLUSION

BDC is a premalignant condition. Our findings show that gallbladder wall thickness > 0.3 cm and Todani type IV are independent risk factors for preoperative carcinogenesis of BDC. They are therefore useful for deciding on the appropriate treatment strategy, especially in asymptomatic patients.

Predictive factors for central lymph node metastases in papillary thyroid microcarcinoma

Papillary thyroid microcarcinoma (PTMC) measures 1 cm or less in its longest dimension. The incidence of PTMC is increasing worldwide. Surgery is the primary treatment; however, prophylactic central lymph node dissection is controversial, and discrepancies between different guidelines have been noted. Routine prophylactic central lymph node dissection may result in hypoparathyroidism and recurrent laryngeal nerve injury in some patients without lymph node metastasis, while simple thyroidectomy may leave metastatic lymph nodes in high-risk patients. To selectively perform prophylactic lymph node dissections in high-risk patients, it is important to identify predictive factors for lymph node metastases in patients with PTMC. Several studies have reported on this, but their conclusions are not entirely consistent. Several clinicopathologic characteristics have been identified as risk factors for central lymph node metastases, and the most commonly reported factors include age, gender, tumor size and location, multifocality, bilaterality, extrathyroidal extension, and abnormal lymph node found using ultrasound. Here, we provide an overview of previous studies along with a favorable opinion on or against these factors, with the aim of increasing the understanding of this topic among the medical community. In addition, current opinions about prophylactic central lymph node dissection are reviewed and discussed.

[Epidemiological characteristics of amoebic dysentery in China, 2015-2018]

Objective: To understand the characteristics and changes of the incidence of amoebic dysentery in China during 2015-2018, explore the causes of high incidence in some areas and provide a data base for the development of national prevention and control strategies and measures. Methods: Data were collected from the infectious disease reporting management information system from Chinese Disease Control and Prevention. To understand the seasonal, population and area distributions of amoebic dysentery, descriptive epidemiological method and software SPSS 16.0 were used to analyze the amoebic dysentery data. Results: A total of 4 366 amoebic dysentery cases were reported without death in China during 2015-2018. The reported average annual incidence was 0.08/100 000, and the overall proportion of laboratory confirmed cases was 68.23%(2 979/4 366). Amoeba dysentery mainly occurred during May to October. One seasonal peak was observed in 2015 and 2017 (July and June, respectively), and two seasonal peaks were observed in 2016 and 2018 (June and October). The patients were mainly children aged under 5 years (42.28%, 1 846/4 366), and the incidence rate decreased with age in children aged under 10 years. Of these, children under 1 years of age had the highest incidence rate (1.28/100 000). The number of cumulative reported cases in Guangxi, Henan, Guangdong, Heilongjiang and Jiangxi provinces ranked top five from 2015-2018, accounting for 64.50% (2 816/4 366) of the total. The cumulative cases in Dongxing county, Guangxi, in Suixian county, Henan and in Ranghulu district, Heilongjiang, respectively accounted for more than 50.00% of the total number of cases in their provinces. Conclusions: The incidence rate of amoebic dysentery reported in China during 2015-2018 showed a decreasing trend, with a higher incidence in children under 5 years old and a higher number of cases in some areas. It is suggested to further investigate and analyze the diagnosis and reporting of amoeba dysentery in key areas and promote the update of the diagnostic standards for amoeba dysentery.

Schwannoma originating from the recurrent laryngeal nerve in a thyroid cancer patient: A case report and review of the literature

BACKGROUND

Schwannoma rarely originates from the recurrent laryngeal nerve, and there are few reports on schwannoma originating from the recurrent nerve in the mediastinum. Herein, we present an extremely rare case of schwannoma originating from the recurrent laryngeal nerve in the neck.

CASE SUMMARY

This is a case report of one patient diagnosed with thyroid cancer with schwannoma originating from the recurrent laryngeal nerve in the neck, which was incidentally found during a thyroidectomy, and a review of the literature.

CONCLUSION

Preoperative diagnostic examinations are of less use for detecting schwannoma originating from a recurrent laryngeal nerve in the neck in such small size, which may only incidentally be found during a thyroidectomy. Surgical excision with opening the capsule and shelling out the tumor is the treatment of choice. If the nerve is unable to be preserved, end-to-end recurrent laryngeal nerve anastomosis may be a simple and minimally invasive reconstruction procedure to improve phonation.

[Epidemiological characteristics of Kala-azar disease in China, during 2005-2015]

Objective: To explore the epidemiological characteristics of Kala-azar disease in China from 2005 to 2015, to provide evidence for the development of related control and measurement strategies. Methods: Data was obtained from Disease Reporting Information System of China CDC, to compare factors on type, distribution, peak season and the age of onset of the cases. Results: Epidemic of Kala-azar had been persistent in China. Number of the reported cases declined in Sichuan and Gansu provinces but two outbreaks had occurred in Xinjiang Uygur autonomous region. The epidemic was confined in few areas. The reported cases were mainly from Xinjiang, Gansu and Sichuan, with the total cases in these three provinces accounted for 95.29% of all the cases seen in the country. The main peak season was from October to November, followed by April. There were significant differences seen in the age distributions of canine Kala-azar, anthroponotic Kala-azar and wildlife-oriented Kala-azar (P<0.05) cases. Majority of the cases involved under 3-year-olds, with peak age in under 1-year-olds for wildlife-oriented Kala-azar. For anthroponotic and canine Kala-azar cases, most of them were seen among the under 10 years old, with the peak among the 5-year-olds. Conclusions: In recent years,Kala-azar had been seen endemic and persistent, in the mid-west regions of China, but with different epidemiological characteristics. Further study on Kala-azar should be carried on to include appropriate measurements and strategies, according to the features of the disease, in the mid-western areas of China.

Outbreak of Occupational Brucellosis at a Pharmaceutical Factory in Southeast China

Brucellosis is an occupational disease affecting workers in butcher shops, the milking and dairy product industry, causing more than 500 000 new cases around the world. As a national statutory B infectious disease in China, morbidity of brucellosis is rapidly increasing in recent years. We report an occupational outbreak of brucellosis infection in a pharmaceutical factory. Exposure was a result of manual operation in the process line, close contact with sheep placentas, insufficient disinfection and repeated using of protective suits and infected by aerosol dissemination. Improved preventive methods, appropriate public health measures and spread of health education would be helpful to prevent the occupational outbreak of brucellosis in future.

Risk Factors for Nodal Metastasis in cN0 Papillary Thyroid Microcarcinoma

BACKGROUND

Despite the majority of papillary thyroid microcarcinoma (PTMC) patients having an excellent prognosis, cervical lymph node metastases are common. The purpose of this study was to investigate the incidence and the predictive risk factors for occult central compartment lymph node metastasis (CLNM) in PTMC patients.

MATERIALS AND METHODS

178 patients with clinically node-negative (cN0) PTMC undergoing prophylactic central compartment neck dissection in our hospital from January 2008 to Jun 2010 were enrolled. The relationship between CLNM and the clinical and pathological factors such as gender, age, tumor size, tumor number, tumor location, extracapsular spread (ECS), and coexistance of chronic lymphocytic thyroiditis was analyzed.

RESULTS

Occult CLNM was observed in 41% (73/178) of PTMC patients. Multivariate analysis showed that male gender, tumor size (≥6mm) and ECS were independent variables predictive of CLNM in PTMC patients.

CONCLUSIONS

Male gender, tumor size (≥6mm) and ECS were risk factors of CLNM. We recommend a prophylactic central lymph node dissection (CLND) should be considered in PTMC patients with such risk factors.

Choledochoduodenal fistula caused by migration of endoclip after laparoscopic cholecystectomy

The wide use of surgical endoclips in laparoscopic surgery has led to a variety of complications. Post-cholecystectomy endoclips migrating into the common bile duct after laparoscopic cholecystectomy is rare. A migrated endoclip can cause obstruction, serve as a nidus for stone formation, and cause cholangitis. While the exact pathogenesis is still unknown, it is probably related to improper clip application, subclinical bile leak, inflammation, and subsequent necrosis, allowing the clips to erode directly into the common bile duct. We present a case of endoclip migrating into the common bile duct and duodenum, resulting in choledochoduodenal fistula after laparoscopic cholecystectomy and a successful reconstruction of the biliary tract by a hepaticojejunostomy with a Roux-en-Y procedure. This case shows that surgical endoclips can penetrate into the intact bile duct wall through serial maceration, and it is believed that careful application of clips may be the only way to prevent their migration after laparoscopic cholecystectomy.

Ileal duplication mimicking intestinal intussusception: A congenital condition rarely reported in adult

Intestinal duplication is an uncommon congenital condition in young adults. A 25-year-old man complained of chronic, intermittent abdominal pain for 3 years following previous appendectomy for the treatment of suspected appendicitis. Abdominal discomfort and pain, suggestive of intestinal obstruction, recurred after operation. A tubular mass was palpable in the right lower quadrant. Computed tomography enterography scan identified suspicious intestinal intussusception, while Tc-99m pertechnetate scintigraphy revealed a cluster of strip-like abnormal radioactivity in the right lower quadrant. On exploratory laparotomy, a tubular-shaped ileal duplication cyst was found arising from the mesenteric margin of the native ileal segment located 15 cm proximal to the ileocecal valve. Ileectomy was performed along with the removal of the duplication disease, and the end-to-end anastomosis was done to restore the gastrointestinal tract continuity. Pathological examination showed ileal duplication with ectopic gastric mucosa. The patient experienced an eventless postoperative recovery and remained asymptomatic within 2 years of postoperative follow-up.

A long adult intussusception secondary to transverse colon cancer

The occurrence of adult intussusception arising from colorectal cancer is quite rare. We present the case of a 76-year-old man with sudden abdominal pain and vomiting. Clinical symptoms included severe abdominal distension and tenderness. Computed tomography scan of the abdomen revealed left-sided colocolic intussusception with a lead point. The patient underwent a left hemicolectomy with right transverse colostomy. Pathologic evaluation revealed moderately differentiated adenocarcinoma invading the muscularis propria; the regional lymph nodes were negative for cancer cells. The postoperative course was uneventful.

Trends in the exploration of anticancer targets and strategies in enhancing the efficacy of drug targeting

A number of therapeutic targets have been explored for developing anticancer drugs. Continuous efforts have been directed at the discovery of new targets as well as the improvement of therapeutic efficacy of agents directed at explored targets. There are 84 and 488 targets of marketed and investigational drugs for the treatment of cancer or cancer related illness. Analysis of these targets, particularly those of drugs in clinical trials and US patents, provides useful information and perspectives about the trends, strategies and progresses in targeting key cancer-related processes and in overcoming the difficulties in developing efficacious drugs against these targets. The efficacy of anticancer drugs directed at these targets is frequently compromised by counteractive molecular interactions and network crosstalk, negative and adverse secondary effects of drugs, and undesired ADMET profiles. Multi-component therapies directed at multiple targets and improved drug targeting methods are being explored for alleviating these efficacy-reducing processes. Investigation of the modes of actions of these combinations and targeting methods offers clues to aid the development of more effective anticancer therapies.

Trends in the exploration of anticancer targets and strategies in enhancing the efficacy of drug targeting

A number of therapeutic targets have been explored for developing anticancer drugs. Continuous efforts have been directed at the discovery of new targets as well as the improvement of therapeutic efficacy of agents directed at explored targets. There are 84 and 488 targets of marketed and investigational drugs for the treatment of cancer or cancer related illness. Analysis of these targets, particularly those of drugs in clinical trials and US patents, provides useful information and perspectives about the trends, strategies and progresses in targeting key cancer-related processes and in overcoming the difficulties in developing efficacious drugs against these targets. The efficacy of anticancer drugs directed at these targets is frequently compromised by counteractive molecular interactions and network crosstalk, negative and adverse secondary effects of drugs, and undesired ADMET profiles. Multi-component therapies directed at multiple targets and improved drug targeting methods are being explored for alleviating these efficacy-reducing processes. Investigation of the modes of actions of these combinations and targeting methods offers clues to aid the development of more effective anticancer therapies.

Unsuspected gallbladder cancer management during or after laparoscopic cholecystectomy

AIM: To explore the effectiveness of surgeons in determining the unsuspected gallbladder carcinoma (UGC) at laparoscopic cholecystectomy (LC) and the management of UGC.

METHODS: A total of 6429 patients with gallbladder disease were included in this study who underwent LC during June, 1989 and November, 2008. Patients with UGC were reviewed retrospectively to assess preoperative diagnosis, intraoperative findings and outcomes.

RESULTS: Of the total patients, 27 in 6429 (0.4%) were histopathologically diagnosed as UGC during (17) or after (10) LC. The tumor stages of the 27 diagnosed were pT₁ (9), pT₂ (9), and pT₃ (91), each with 9 cases. The survival rates of all the UCG patients in one-year, three-year and five-year were 74.1%, 63% and 59.3%, respectively. The five-year survival rates of pT₁ stage, pT₂ stage and pT₃ stage were 100%, 66.7% and 0.0%, respectively, not significantly affected by whether the patients had been diagnosed with UGC during or after LC (P < 0.05).

CONCLUSION: The survival rate from UGC is associated with tumor stage and it is confirmed that a carefully performed LC is adequate treatment for pT₁ stage cancer. If a suspicious lesion is found, intraoperative frozen section is performed for pathological examination. However, radical operation is recommended for T₂ patients and effective measures should be taken to avoid tumor implant and metastasis.

Trends in the exploration of therapeutic targets for the treatment of endocrine, metabolic and immune disorders

A number of therapeutic targets have been explored for developing drugs in the treatment of endocrine, metabolic and immune disorders. Continuous efforts and increasing interest have been directed at the search of new targets. Data from the therapeutic target database at http://bidd.nus.edu.sg/group/cjttd/ttd.asp, shows that there are 26, 24, and 22 targets of marketed drugs for the treatment of these three classes of diseases, respectively. The number of targets of investigational agents has reached 98, 124, and 72, respectively. An analysis of these targets, particularly those of recently approved drugs and patented investigational agents, provides useful hint about the general trends of target exploration, with current focus on drug discovery and the difficulties encountered in developing drugs against these targets. Multiple profiles of these targets have been analyzed to probe the sequence, structural, physicochemical and systems-related features contributing to the successful exploration of a target against these diseases.

Occupational Medicine Physicians in the United States: Demographics and Core Competencies

OBJECTIVE

We assessed the demographic profile and opinions of current occupational medicine (OM) physicians on the importance of specific core competencies.

METHODS

A random sample of 1500 OM physicians listed in the membership directory of the American College of Occupational and Environmental Medicine (ACOEM) were asked to complete a voluntary survey.

RESULTS

Six hundred and ten OM physicians completed the survey. Fifty two percent worked in clinical settings, and 16% worked in corporate or industrial settings. Eighty percent were satisfied with their choice of careers.

CONCLUSIONS

OM physicians appeared to be highly trained, with 60% certified in OM and 68% board certified in other specialties. The OM physicians valued staying current in the field, understanding the relationship between occupational exposure and health, and communicating with stakeholders most highly. Occupational physicians are an important source of knowledge regarding what competencies and core knowledge areas are important for OM practice.

Therapeutic targets: progress of their exploration and investigation of their characteristics

Modern drug discovery is primarily based on the search and subsequent testing of drug candidates acting on a preselected therapeutic target. Progress in genomics, protein structure, proteomics, and disease mechanisms has led to a growing interest in and effort for finding new targets and more effective exploration of existing targets. The number of reported targets of marketed and investigational drugs has significantly increased in the past 8 years. There are 1535 targets collected in the therapeutic target database compared with approximately 500 targets reported in a 1996 review. Knowledge of these targets is helpful for molecular dissection of the mechanism of action of drugs and for predicting features that guide new drug design and the search for new targets. This article summarizes the progress of target exploration and investigates the characteristics of the currently explored targets to analyze their sequence, structure, family representation, pathway association, tissue distribution, and genome location features for finding clues useful for searching for new targets. Possible "rules" to guide the search for druggable proteins and the feasibility of using a statistical learning method for predicting druggable proteins directly from their sequences are discussed.

Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties

Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational methods have been developed for predicting MHC-binding peptides, which achieve impressive prediction accuracies of 70-90% for binders and 40-80% for non-binders. These methods have been developed for peptides of fixed lengths, for a limited number of alleles, trained from small number of non-binders, and in some cases based straightforwardly on sequence. These limit prediction coverage and accuracy particularly for non-binders. It is desirable to explore methods that predict binders of flexible lengths from sequence-derived physicochemical properties and trained from diverse sets of non-binders. This work explores support vector machines (SVM) as such a method for developing prediction systems of 18 MHC class I and 12 class II alleles by using 4208-3252 binders and 234,333-168,793 non-binders, and evaluated by an independent set of 545-476 binders and 110,564-84,430 non-binders. Binder accuracies are 86-99% for 25 and 70-80% for 5 alleles, non-binder accuracies are 96-99% for 30 alleles. Binder accuracies are comparable and non-binder accuracies substantially improved against other results. Our method correctly predicts 73.3% of the 15 newly-published epitopes in the last 4 months of 2005. Of the 251 recently-published HLA-A*0201 non-epitopes predicted as binders by other methods, 63 are predicted as binders by our method. Screening of HIV-1 genome shows that, compared to other methods, a comparable percentage (75-100%) of its known epitopes is correctly predicted, while a lower percentage (0.01-5% for 24 and 5-8% for 6 alleles) of its constituent peptides are predicted as binders. Our software can be accessed at .

Prediction of compounds with specific pharmacodynamic, pharmacokinetic or toxicological property by statistical learning methods

Computational methods for predicting compounds of specific pharmacodynamic, pharmacokinetic, or toxicological property are useful for facilitating drug discovery and drug safety evaluation. The quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) methods are the most successfully used statistical learning methods for predicting compounds of specific property. More recently, other statistical learning methods such as neural networks and support vector machines have been explored for predicting compounds of higher structural diversity than those covered by QSAR and QSPR. These methods have shown promising potential in a number of studies. This article is intended to review the strategies, current progresses and underlying difficulties in using statistical learning methods for predicting compounds of specific property. It also evaluates algorithms commonly used for representing structural and physicochemical properties of compounds.

Prediction of the functional class of lipid binding proteins from sequence-derived properties irrespective of sequence similarity

Lipid binding proteins play important roles in signaling, regulation, membrane trafficking, immune response, lipid metabolism, and transport. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting lipid binding proteins irrespective of sequence similarity. This work explores the use of support vector machines (SVMs) as such a method. SVM prediction systems are developed using 14,776 lipid binding and 133,441 nonlipid binding proteins and are evaluated by an independent set of 6,768 lipid binding and 64,761 nonlipid binding proteins. The computed prediction accuracy is 78.9, 79.5, 82.2, 79.5, 84.4, 76.6, 90.6, 79.0, and 89.9% for lipid degradation, lipid metabolism, lipid synthesis, lipid transport, lipid binding, lipopolysaccharide biosynthesis, lipoprotein, lipoyl, and all lipid binding proteins, respectively. The accuracy for the nonmember proteins of each class is 99.9, 99.2, 99.6, 99.8, 99.9, 99.8, 98.5, 99.9, and 97.0%, respectively. Comparable accuracies are obtained when homologous proteins are considered as one, or by using a different SVM kernel function. Our method predicts 86.8% of the 76 lipid binding proteins nonhomologous to any protein in the Swiss-Prot database and 89.0% of the 73 known lipid binding domains as lipid binding. These findings suggest the usefulness of SVMs for facilitating the prediction of lipid binding proteins. Our software can be accessed at the SVMProt server (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi).

Prediction of functional class of novel bacterial proteins without the use of sequence similarity by a statistical learning method

A substantial percentage of the putative protein-encoding open reading frames (ORFs) in bacterial genomes have no homolog of known function, and their function cannot be confidently assigned on the basis of sequence similarity. Methods not based on sequence similarity are needed and being developed. One method, SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi), predicts protein functional family irrespective of sequence similarity (Nucleic Acids Res. 2003;31:3692-3697). While it has been tested on a large number of proteins, its capability for non-homologous proteins has so far been evaluated for a relatively small number of proteins, and additional tests are needed to more fully assess SVMProt. In this work, 90 novel bacterial proteins (non-homologous to known proteins) are used to evaluate the capability of SVMProt. These proteins are such that none of their homologs are in the Swiss-Prot database, their functions not clearly described in the literature, and they themselves and their homologs are not included in the training sets of SVMProt. They represent proteins whose function cannot be confidently predicted by sequence similarity methods at present. The predicted functional class of 76.7% of each of these proteins shows various levels of consistency with the literature-described function, compared to the overall accuracy of 87% for the SVMProt functional class assignment of 34,582 proteins that have at least one homolog of known function. Our study suggests that SVMProt is capable of assigning functional class for novel bacterial proteins at a level not too much lower than that of sequence alignment methods for homologous proteins.

PEARLS: Program for Energetic Analysis of Receptor−Ligand System

Analysis of the energetics of small molecule ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions facilitates the quantitative understanding of molecular interactions that regulate the function and conformation of proteins. It has also been extensively used for ranking potential new ligands in virtual drug screening. We developed a Web-based software, PEARLS (Program for Energetic Analysis of Ligand-Receptor Systems), for computing interaction energies of ligand-protein, ligand-nucleic acid, protein-nucleic acid, and ligand-protein-nucleic acid complexes from their 3D structures. AMBER molecular force field, Morse potential, and empirical energy functions are used to compute the van der Waals, electrostatic, hydrogen bond, metal-ligand bonding, and water-mediated hydrogen bond energies between the binding molecules. The change in the solvation free energy of molecular binding is estimated by using an empirical solvation free energy model. Contribution from ligand conformational entropy change is also estimated by a simple model. The computed free energy for a number of PDB ligand-receptor complexes were studied and compared to experimental binding affinity. A substantial degree of correlation between the computed free energy and experimental binding affinity was found, which suggests that PEARLS may be useful in facilitating energetic analysis of ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions. PEARLS can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/rune.pl.

Prediction of functional class of novel plant proteins by a statistical learning method

In plant genomes, the function of a substantial percentage of the putative protein-coding open reading frames (ORFs) is unknown. These ORFs have no significant sequence similarity to known proteins, which complicates the task of functional study of these proteins. Efforts are being made to explore methods that are complementary to, or may be used in combination with, sequence alignment and clustering methods. A web-based protein functional class prediction software, SVMProt, has shown some capability for predicting functional class of distantly related proteins. Here the usefulness of SVMProt for functional study of novel plant proteins is evaluated. To test SVMProt, 49 plant proteins (without a sequence homolog in the Swiss-Prot protein database, not in the SVMProt training set, and with functional indications provided in the literature) were selected from a comprehensive search of MEDLINE abstracts and Swiss-Prot databases in 1999-2004. These represent unique proteins the function of which, at present, cannot be confidently predicted by sequence alignment and clustering methods. The predicted functional class of 31 proteins was consistent, and that of four other proteins was weakly consistent, with published functions. Overall, the functional class of 71.4% of these proteins was consistent, or weakly consistent, with functional indications described in the literature. SVMProt shows a certain level of ability to provide useful hints about the functions of novel plant proteins with no similarity to known proteins.

Trends in exploration of therapeutic targets

Lead discovery against a preselected therapeutic target is a key component in modern drug development. Continuous effort and increasing interest has been directed at the search for new targets, which has led to the identification of a growing number of them. Data from the therapeutic target database, at http://bidd.nus.edu.sg/group/cjttd/ttd.asp, show that, as of July 2004, the number of documented targets of marketed and investigational drugs has reached 1,174 distinct proteins (including subtypes) and 27 nucleic acids, 239 of which are targets of the marketed drugs. Analysis of these targets, particularly those of recently approved drugs and patented investigational agents, provide useful hints about general trends of target exploration and current focus in drug discovery for the treatment of high impact diseases needing effective or more treatment options.

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids

Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.

TRMP: a database of therapeutically relevant multiple pathways

Disease processes often involve crosstalks between proteins in different pathways. Different proteins have been used as separate therapeutic targets for the same disease. Synergetic targeting of multiple targets has been explored in combination therapy of a number of diseases. Potential harmful interactions of multiple targeting have also been closely studied. To facilitate mechanistic study of drug actions and a more comprehensive understanding the relationship between different targets of the same disease, it is useful to develop a database of known therapeutically relevant multiple pathways (TRMPs). Information about non-target proteins and natural small molecules involved in these pathways also provides useful hint for searching new therapeutic targets and facilitate the understanding of how therapeutic targets interact with other molecules in performing specific tasks. The TRMPs database is designed to provide information about such multiple pathways along with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, structural and functional information about each protein in the pathways. Cross links to other databases are also introduced to facilitate the access of information about individual pathways and proteins.

AVAILABILITY

This database can be accessed at http://bidd.nus.edu.sg/group/trmp/trmp.asp and it currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions together with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name.

SUPPLEMENTARY INFORMATION

http://bidd.nus.edu.sg/group/trmp/sm.pdf

Modeling the maternal-age dependency of reproductive failure and genetic fitness

The offspring of older parents are at a higher risk of suffering low birth weights and congenital birth defects that result from mutations and chromosomal anomalies. When the defect is paternal in origin, it often can be shown that the primary lesion arose during mitotic proliferation of the spermatogonial germ cell population. By contrast, germline mosaicism is seldom invoked to explain the age dependency of maternally derived aberrations because germline proliferation in the ovary is already completed during fetal development. Age-dependent defects of maternal origin might, however, be explained in part by the progressive loss of oocytes during the mother's reproductive life. A large number of oocytes undergo the initial stages of maturation each month, but typically only one completes maturation and is ovulated while the majority are discarded, probably by an apoptotic mechanism. Here we explore the possibility that the monthly choice of oocytes to undergo maturation is influenced by subtle phenotypic characters of those oocytes that may bear genetic defects such as trisomy 21. We have generated a mathematical model to describe the loss kinetics for such mutant oocytes relative to the overall pool of resting oocytes, and we assess evolutionary strategies that would favor their utilization faster than, at the same rate as, or slower than the normal oocytes. This formulation reveals that the slower-rate scheme would effectively diminish the utilization of mutant oocytes in young mothers but would increase the risk of related birth defects for older mothers. Accordingly, we propose that natural selection should have favored the delayed utilization of defective oocytes in a primitive high-mortality culture, but that this evolutionary strategy would be outmoded for modern society, because it would lead to an increased frequency of birth defects for older mothers.

Threshold distributions of phenylthiocarbamide (PTC) in the Chinese population

The ability to taste phenylthiocarbamide (PTC) is a well-documented Mendelian trait. Mapping and cloning the gene(s) responsible for the PTC tasting ability would help to delineate the molecular basis for the variations in PTC tasting ability in humans and to shed new light on taste chemosensory functions. In view of the spectacular successes in genome science, the positional cloning strategy seems to be a feasible approach to the isolation of the gene(s) underlying the PTC tasting ability. As a first step toward mapping the gene(s), we collected PTC taste threshold data on 106 individuals, most of them being university students, in Shanghai, China. Using various parametric and nonparametric statistical methods, we have found that the data set is best described by a bimodal distribution. The frequency of PTC nontasters is estimated to be 10%. This is consistent with the view that the PTC nontasting ability follows a recessive mode of inheritance. Several authors had previously reported PTC data on Chinese living outside China. Our data are, to our knowledge, the first ever collected from the Chinese population within China.

Comparison of the Green scale versus magnitude estimation for taste perception

The Green scale is a new psychophysical method that is simple for subjects to use, but its relation with magnitude estimation has yet to be fully characterized. In comparing the consistency between the Green scale and magnitude estimation, we found that the former seems to provide a psychological oral sensation measurement that is different from the latter method. A simple correction formula can be derived.

Development of 124 sequence-tagged sites and cytogenetic localization of 217 cosmids for human chromosome 10

A total of 124 new chromosome 10-specific sequence-tagged sites (STSs) were derived from two sources: (1) DNA sequences obtained from anonymous clones in new libraries enriched for human chromosome 10 inserts, and (2) published sequences of genes and other loci already known to map to chromosome 10. Libraries were constructed from a somatic cell hybrid carrying human chromosomes 10 and Y. A cosmid library was made from total DNA of the hybrid and probed with labeled total human DNA to identify clones with human DNA inserts. Two hundred seventeen cosmids were mapped to regions of human chromosome 10 by fluorescence in situ hybridization. Twenty-five cosmids represent probes that have been placed on the genetic map previously. One hundred ninety-two cosmids represent new probes that have not been mapped previously. Cosmids carrying inserts with CA repeats were identified by hybridization with a labeled poly(dC-dA)-poly(dG-dT) probe and subcloned to yield microsatellite STS markers. Two small insert plasmid libraries were made, the first by subcloning inserts from a chromosome 10-enriched lambda phage library (LL10NS01) and the second by cloning Alu element-mediated PCR products amplified from hybrid DNA. STSs were generated from the DNA sequences of clone inserts. Chromosome 10-specific STSs were distinguished from Y chromosome STSs by one or both of the following criteria: (1) successful PCR amplification from a template consisting of DNA from another chromosome 10-containing cell line, NA10926B, or (2) FISH localization to chromosome 10 of the source cosmid or of YACs isolated by PCR screening with the STS. These libraries were the source of 90 new chromosome 10-specific STSs, 42 of which contain CA repeats.

[Diagnosis and treatment of presacral tumors: report of 28 cases]

Tumors in presacral space are uncommon. From 1980-1991, 28 patients with presacral tumors underwent surgical operation at PUMC Hospital. Most tumors are of the congenital type (epidermoid, teratoma and chordoma). 9 patients had no symptoms and their tumors were found on routine anal examination. Ultrasound and CT scans had been proved valuable in the diagnosis of presacral tumors. The tumor was completely resected in 23, incompletely resected in 2 without operative mortality. The diagnosis and surgical management of presacral tumors were discussed.

Allelic instability in mitosis: a unified model for dominant disorders

Recent findings indicate that tandemly repeated triplet sequences in certain disease-causing human genes may render these genes highly unstable not only in meiosis but also in mitosis. Typically, a dominant mutation arises upon expansion in the number of these repeated elements. We have considered how mitotic instability of this sort might affect both phenotypic expression and allele transmission. A model based on these considerations leads to the following predictions: (i) Phenotypic severity among individuals who inherit an unstable allele should be highly variable due to stochastic variation in the stage of its earliest mutagenic expansion. (ii) Strikingly increased severity or decreased age of onset in some offspring should arise because of parental germ-line mosaicism for an expanded or mutant allele. (iii) The magnitude of genetic anticipation should be more strongly correlated with paternal than with maternal age at the time of conception. (iv) Given a child born with a severe phenotype, the recurrence risk for a second severely affected child should be significantly elevated. (v) The severity of phenotype in a child should be positively correlated with that in a parent. Available data on fragile X syndrome, Huntington disease, and myotonic dystrophy are shown to be consistent with the model, and implications for an understanding of achondroplasia and other dominant disorders are discussed.

Oocyte selection: a new model for the maternal-age dependence of Down syndrome

Previously proposed mechanisms for Down syndrome (trisomy 21) have generally invoked a progressive increase in meiotic nondisjunction to explain maternal-age dependence, but models of this sort have failed to predict the observed patterns of marker segregation. Here we propose instead that age-dependent trisomy 21 results primarily from a mechanism that favors maturation and utilization of euploid oocytes in preference to the pre-existing aneuploid products of mitotic (premeiotic) nondisjunction. The increased utilization of aneuploid oocytes at later stages of maternal life would result from their increased proportion following many progressive cycles of selection against their maturation in earlier stages. Derivation of a quantitative model and evaluation of existing data indicate that the pattern of marker segregation associated with age-dependent trisomy 21 supports the proposed mechanism.