Neuroprotective effect of salidroside on hippocampal neurons in diabetic mice via PI3K/Akt/GSK-3β signaling pathway

BACKGROUND

Diabetic encephalopathy is manifested by cognitive dysfunction. Salidroside, a nature compound isolated from Rhodiola rosea L, has the effects of anti-inflammatory and antioxidant, hypoglycemic and lipid-lowering, improving insulin resistance, inhibiting cell apoptosis, and protecting neurons. However, the mechanism by which salidroside alleviates neuronal degeneration and improves learning and memory impairment in diabetic mice remains unclear.

OBJECTIVE

To investigate the effects and mechanisms of salidroside on hippocampal neurons in streptozotocin-induced diabetic mice.

MATERIALS AND METHODS

C57BL/6 mice were randomly divided into 4 groups to receive either sham (control group (CON)), diabetes mellitus (diabetes group (DM)), diabetes mellitus + salidroside (salidroside group (DM + SAL)), and diabetes mellitus + salidroside + phosphatidylinositol 3-kinase (PI3K) inhibitor LY294002 (diabetes mellitus + salidroside + LY294002 group (DM + SAL + LY294002)). After 12 weeks of diabetes onset, the cognitive behaviors were tested using Morris water maze. The number of hippocampal neurons was detected by Nissl staining. The expressions of PI3K, p-PI3K, Akt, p-Akt, GSK-3β, p-GSK-3β, cleaved caspase-3, caspase-3, Bax, Bcl-2, MAP2, and SYN in the hippocampus were detected by Western blot. Moreover, the expression of MAP2 and SYN in the hippocampus was further confirmed by immunofluorescence staining.

RESULTS

Salidroside increased the time of diabetic mice in the platform quadrant and reduced the escape latency of diabetic mice. Salidroside also increased the expression of p-PI3K, p-Akt, p-GSK-3β, MAP2, SYN, Bcl-2, while suppressed the expression of cleaved caspase-3, caspase3, and Bax in the DM + SAL group compared with the DM group (P < 0.05). The Nissl staining showed that the number of hippocampus neurons in the DM + SAL group was increased with the intact, compact, and regular arrangement, compared with the DM groups (P < 0.05). Interestingly, the protective effects of salidroside on diabetic cognitive dysfunction, hippocampal morphological alterations, and protein expressions were abolished by inhibition of PI3K with LY294002.

CONCLUSIONS

Salidroside exerts neuroprotective properties in diabetic cognitive dysfunction partly via activating the PI3K/Akt/GSK-3β signaling pathway.

[The diagnostic performance of 2020 Chinese Ultrasound Thyroid Imaging Reporting and Data System in thyroid nodules]

Objective: To evaluate the diagnostic performance of the Chinese Ultrasound Thyroid Imaging Reporting and Data System (C-TIRADS) in thyroid nodules,and to compare it with the TIRADS proposed by Kwak et al. (K-TIRADS) and the TIRADS proposed by the American College of Radiology (ACR-TIRADS). Methods: The data of 1 750 patients with 2 029 thyroid nodules in the Department of Thyroid Surgery, the Affiliated Hospital of Jining Medical University from January 2018 to November 2020 was retrospectively collected. Among them, there were 328 males and 1 422 females,aged from 6 to 86 with an average of (47±12) years. The nodules were divided into≤1.0 cm group(n=997) and>1.0 cm group(n=1 032)based on the size of the nodules. The stratification for malignant risk and the determination of benign or malignancy of the nodules was evaluated using the C-TIRADS, K-TIRADS and ACR-TIRADS, respectively. The receiver operating characteristic (ROC)curve analysis was performed to compare the diagnostic performance of the aforementioned three kinds of TIRADS using pathological results as the referent standard. Results: The optimal diagnosis points in the determination of malignant nodules of C-TIRADS, K-TIRADS and ACR-TIRADS in the two groups were 4A, 4b and 4 respectively according to ROC curve analysis. For the diagnosis of the malignant nodules, the C-TIRADS achieved with an AUC value of 0.772 and 0.892 in the ≤1.0 cm group and>1.0 cm group, respectively, which was significantly higher than K-TIRADS (AUC= 0.762 and 0.869, respectively) and ACR-TIRADS (AUC= 0.735 and 0.832, respectively) (P<0.05). The sensitivity, specificity, accuracy, positive predictive value and negative predictive value of C-TIRADS were 94.99%, 59.41%, 86.46%, 88.13%, 78.89% (≤1.0 cm group)and 88.34%, 90.05%, 89.34%, 86.33%, 91.57%(>1.0 cm group), respectively. C-TIRADS had the highest sensitivity, accuracy, and negative predictive value in the determination of malignant nodules in both groups compared to the other two kinds of TIRADS. Conclusions: The three kinds of TIRADS all have high diagnostic performance for the determination of the malignant nodules, and the C-TIRADS has the best overall efficacy, which can effectively assist clinicians for medical decision, and is worth to be popularized and applied in the clinical setting.

Further characterization of clinical and laboratory features occurring in VEXAS syndrome in a large-scale analysis of multicenter case-series of 116 French patients

BACKGROUND

A new autoinflammatory syndrome related to somatic mutations of UBA1 was recently described and called VEXAS syndrome.

OBJECTIVE

To describe clinical characteristics, laboratory findings and outcomes of VEXAS syndrome.

DESIGN

Case-series.

SETTING

Patients referred to a French multicenter registry between November 2020 and May 2021.

PATIENTS

116 patients with VEXAS syndrome.

MEASUREMENTS

Frequency and median of parameters and vital status, from diagnosis to the end of the follow-up.

RESULTS

Main clinical features were skin lesions (83.5%), non-infectious fever (63.6%), weight loss (62%), lung involvement (49.6%), ocular symptoms (38.8%), relapsing chondritis (36.4%), venous thrombosis (34.7%), lymph nodes (33.9%), and arthralgia (27.3%). Hematological disease was present in 58 cases (50%), considered as myelodysplastic syndrome (MDS, n= 58) and monoclonal gammapathy of unknown significance (n=12).UBA1 mutations included p.M41T (44.8%), p.M41V (30.2%), p.M41L (18.1%), and splice mutations (6.9%). After a median follow-up of 3.0 years, 18 patients died (15.5%), from infectious origin (n=9) and MDS progression (n=3). Unsupervised analysis identified 3 clusters: cluster 1 (47%) with mild-to-moderate disease; cluster 2 (16%) with underlying MDS and higher mortality rates; cluster 3 (37%) with constitutional manifestations, higher C-reactive protein levels and less frequent chondritis. Five-year probability of survival was 84.2% in cluster 1, 50.5 % in cluster 2, and 89.6% in cluster 3. UBA1 p.Met41Leu mutation was associated with a better prognosis.

CONCLUSION

VEXAS syndrome displays a large spectrum of organ manifestations and shows different clinical and prognostic profiles. It also raises a potential impact of the identified UBA1 mutation.

[Analysis of genetic characteristics in two Chinese children of type Ⅱ Waardenburg syndrome]

Objective: To screen and analyze the mutations of MITF gene in two children of type Ⅱ Waardenburg syndrome (WS2) from different families in Yunnan,China,and to explore the possible molecular pathogenesis. Methods: With informed consent, medical history collection, physical examinations, audiological evaluation, and high resolution computer tomography (HRCT) scan of temporal bone were performed on the two WS2 probands and their family members. Genomic DNA was extracted from peripheral blood of all individuals. The coding regions including all exons, part of introns and promoters of MITF, PAX3, SOX10, SNAI2, END3, ENDRB, and KITLG genes were sequenced by high-throughput sequencing. According to the results of high-throughput sequencing, pathogenic mutations detected in the probands and their parents were verified by Sanger sequencing. Results: The proband 1 carried c.641_643delGAA mutation in the 7th exon of MITF gene, which was a frame-shift mutation resulting in an amino acid change of p.214delR. It was a de novo mutation as the parents of proband 1 showed no variation on this site. The proband 2 carried heterozygous loss of the large fragment ranging from exon 1 to exon 9 of MITF gene, which defected the function of MITF protein. Conclusion: Genetic examinations provide important evidence for diagnosis of Waardenburg syndrome. Heterozygous mutation c.641_643delGAA and heterozygous loss of the large fragment ranging from exon 1 to exon 9 of MITF gene might be the molecular pathogenesis of the two WS2 probands in this study.

[Analysis of genotypes and audiological characteristics of children with SLC26A4 gene pathogenic mutations]

Objective:To explore the correlation of SLC26A4 genotype and audiology.Method:The subjects were 70 children aged 0 to 7 years old, who were admitted to otological outpatient department.All subjects received nine crystal hereditary deafness gene chip and confirmed by (or)SLC26A4 gene full coding region detection.The patients were diagnosed as homozygous or compound heterozygous mutations.At the same time,acoustic immittance,auditory brainstem response, auditory steady state response and pediatric behavior audiometry, newborn hearing screening and other audiological tests were displayed. According to the genotype, the subjects were divided into two groups: group A (SLC26A4 gene homozygous mutation) in 40 cases, group B (SLC26A4 gene compound heterozygous mutation) in 30 cases. The frequency of SLC26A4 gene mutation, the two groups of genotypes and hearing screening results,the degree of hearing loss and audiometric configurations were analyzed statistically. Result: In 70 patients, the top 4 of the 70 patients with high frequency of mutations were IVS7-2A> G(76.43%), 2168A> G(15.00%), 1226G> A(2.86%) and 2000T> C(2.16%), respectively. 34.29% of newborns passed hearing screening with single or double ears, among which group A and group B were 32.50% and 36.67%,respectively. There was no statistically significant difference between two groups in hearing screening. The degree of hearing loss in group A(56.25%) and group B(48.33%) were mainly profound and there was no significant difference between them. The audiometric configurations: group A(60.00%) was mainly high frequency loss type, while group B(55.00%) was mainly flat type. The difference between them was statistically significant.Conclusion:The mutation sites of SLC26A4 gene were mainly IVS7-2A> G, and the degree of hearing loss was mostly profound. To the audiometric configurations,SLC26A4 gene homozygous mutant were mainly high frequency loss type, while SLC26A4 gene compound heterozygous mutant were mainly flat type. 34.29% children passed universal newborn hearing screening with one ear at least, which indicates SLC26A4 gene mutations can result in late-onset hearing loss, so those patients should be attached great importance..

[Correlation between ultrasonographic optic nerve sheath diameter and intracranial pressure]

Objective: To evaluate the association of the ultrasonographic optic nerve sheath diameter (ONSD) and intracranial pressure (ICP), and the feasibility of ultrasonographic ONSD in predicting high ICP. Methods: A prospective study. The outpatients who planned to measure ICP by lumbar puncture in Department of Neurology, Xuanwu Hospital, Capital Medical University were selected from January 2011 to May 2012. All the retrobulbar ONSD measurement with B-scan ultrasound was performed just before lumbar puncture. When high ICP was defined as ICP more than 200 mmH₂O(1 mmH₂O=0.009 8 kPa), the participants were divided into the high ICP group and the normal ICP group. The Pearson correlation coefficient analysis was used to analyze the correlation between ICP and postbulbar ONSD measurements. The difference in ONSD was compared between the high ICP and normal ICP groups with the t test. The receiver operating characteristic (ROC) curve was used to calculate the cutoff value of mean ONSD and evaluate the sensitivity and specificity of the method. Results: A total of 130 participants were involved in this study. There were 71 males and 59 females, aged (38±14) years.The mean ICP was (209.84±79.99) mmH₂O. The mean ONSD was (5.68±0.78) mm in the right eyes, (5.78±0.78) mm in the left eyes, and (5.73±0.71) mm in both eyes. The ICP had a significant correlation with ONSD in the right eyes (r=0.54, P<0.001), ONSD in the left eyes (r=0.56, P<0.001) and ONSD in both eyes (r=0.60, P<0.001), but no correlation with age (r=-0.14, P=0.114) and gender (r=0.20, P=0.817). The ONSD in the high ICP group (n=65) was (6.11±0.66) mm, (6.22±0.56) mm and (6.17±0.50) mm in the right eyes, left eyes, and both eyes, respectively. Compared with the ONSD in the normal ICP group (n=65), which was (5.26±0.64) mm in the right eyes, (5.34±0.72) mm in the left eyes and (5.30±0.62) mm in both eyes, there was a significantly enlarged ONSD in the high ICP group (t=-7.507, -7.778, -8.779, all P<0.001). The ROC analysis showed the ONSD of 5.6 mm was the best cutoff value with a sensitivity of 86% and a specificity of 71% for identifying high ICP. Conclusions: There is a significantly positive correlation between ICP and postbulbar ONSD measured by ultrasound. This non-invasive method may be an alternative approach to predicting the ICP value of patients whose ICP measurement via lumbar puncture is at high risk. However, it can not replace the direct ICP measurement with the invasive method. (Chin J Ophthalmol, 2018, 54: 683-687).

[Antimicrobial susceptibility and genotyping of Mycobacterium intracellulare]

Objective: To investigate the antimicrobial susceptibility and genotyping of Mycobacterium intracellulare. Methods: A total of 150 M. intracellulare isolates were collected. The susceptibility against 15 antimicrobial agents widely used for treatment of non-tuberculosis mycobacteria (NTM) infections, was tested by broth microdilution assay. Variable number of tandem repeats (VNTR) assay was also performed using the 16-loci genotyping method. Results: The drug susceptibility test revealed that clarithromycin (97.3%, 146/150), moxifloxacin (94.0%, 141/150) and amikacin (90.0%, 135/150) had the best antimicrobial activities in vitro against the M. intracellulare isolates. Secondly, 75.3%(113/150), 64.0%(96/150), 52.7%(79/150) and 8.7%(13/150) of the strains were susceptible to rifampicin, linezolid, capreomycin, and ethambutol, respectively. The MIC(50) and MIC(90) values of the 3 injectable anti-tuberculosis drugs were as follows: amikacin 4 mg/L and 16 mg/L, streptomycin 4 mg/L and 16 mg/L, capreomycin 8 mg/L and 16 mg/L. The MIC(50) and MIC(90) values of the 5 different fluoroquinolones were 0.5 mg/L and 2 mg/L for moxifloxacin , 1 mg/L and 8 mg/L for ciprofloxacin, 1 mg/L and 8ug/ml for levofloxacin, 2 mg/L and 16 mg/L for antoflolxacin, 2 mg/L and 16 mg/L for ofloxacin. The Hunter-Gaston Discriminatory Index (HGDI) value for the 16-loci VNTR typing of M. intracellulare isolates was 0.994. VNTR differentiated the 150 isolates into 21 clusters and acquired a total of 121 unique patterns. Drug resistance profile was not independently associated with cluster strains. Conclusions: Clarithromycin, moxifloxacin and amikacin had the best antimicrobial activities in vitro against M. intracellulare isolates. The 16-loci VNTR typing revealed a highly discriminatory power and drug resistance profile was not independently associated with cluster strains.

[Effects of decline of pH value on cardiomyocyte viability of rats and the mechanism]

Objective: To explore the effects of decline of pH value on cardiomyocyte viability of rats, and to analyze the possible mechanism. Methods: Hearts of five newborn Sprague-Dawley rats were isolated, and then primary cardiomyocytes were cultured and used in the following experiments. (1) The primary cardiomyocytes were divided into pH 7.4+ 6 h, pH 7.0+ 6 h, pH 6.5+ 6 h, pH 6.0+ 6 h, pH 6.5+ 1 h, and pH 6.5+ 3 h groups according to the random number table, with 4 wells in each group. After being routinely cultured for 48 h (similarly hereinafter), cells in pH 7.4+ 6 h, pH 7.0+ 6 h, pH 6.5+ 6 h, and pH 6.0+ 6 h groups were cultured with pH 7.4, pH 7.0, pH 6.5, and pH 6.0 DMEM-F12 medium (similarly hereinafter), respectively, and then they were cultured for 6 h. Cells in pH 6.5+ 1 h and pH 6.5+ 3 h groups were cultured with pH 6.5 medium, and then they were cultured for 1 h and 3 h, respectively. Viability of cells was detected by methyl-thiazolyl-tetrazolium (MTT) method. (2) The primary cardiomyocytes were divided into pH 7.4, pH 6.5, and pH 6.5+ taxol groups according to the random number table, with 2 wells in each group. Cells in pH 7.4 group were cultured with pH 7.4 medium, while cells in pH 6.5 and pH 6.5+ taxol groups were cultured with pH 6.5 medium. Cells in pH 6.5+ taxol group were added with taxol of a final molarity of 0.2 μmol/L in addition, and then they were cultured for 6 h. Morphology and density of microtubule of cells was detected by immunofluorescence assay. (3) The primary cardiomyocytes were grouped and treated as in experiment (2), with 2 wells in each group. The expressions of polymerized microtubulin and free microtubulin were determined with Western blotting. (4) The primary cardiomyocytes were grouped and treated as in experiment (2), with 4 wells in each group. Viability of cells after treated with taxol was detected by MTT method. Data were processed with one-way analysis of variance and LSD-t test. Results: (1) The viability of cells in pH 7.4+ 6 h, pH 7.0+ 6 h, pH 6.5+ 6 h, pH 6.0+ 6 h, pH 6.5+ 1 h, and pH 6.5+ 3 h groups were 1.00±0.08, 0.90±0.08, 0.85±0.06, 0.83±0.04, 0.91±0.10, and 0.89±0.10, respectively. Compared with that in pH 7.4+ 6 h group, viability of cells in pH 7.0+ 6 h, pH 6.5+ 6 h, pH 6.0+ 6 h, pH 6.5+ 1 h, and pH 6.5+ 3 h groups were all decreased in different degrees (t=2.476, 4.002, 4.996, 2.168, 2.400, P<0.05). (2) Microtubules of cells in pH 7.4 group were radially distributed around the nucleus with clear tubular structure. Compared with that in pH 7.4 group, the skeleton of microtubules of cells in pH 6.5 group was obviously damaged, with broken structure of microtubule and reduced density. Compared with that in pH 6.5 group, the damage degree of microtubules of cells in pH 6.5+ taxol group was obviously alleviated, and the structure of microtubules basically returned to normal. (3) Compared with that in pH 7.4 group, the expression of free microtubulin of cells in pH 6.5 group was significantly increased (t=3.030, P<0.05), while the expression of polymerized microtubulin of cells was significantly decreased (t=8.604, P<0.05). Compared with that in pH 6.5 group, the expression of free microtubulin of cells in pH 6.5+ taxol group was significantly decreased (t=4.559, P<0.05), while the expression of polymerized microtubulin of cells was significantly increased (t=5.472, P<0.05). (4) Viability of cells in pH 7.4, pH 6.5, and pH 6.5+ taxol groups were 1.00±0.10, 0.83±0.04, and 0.93±0.10, respectively. Compared with that in pH 7.4 group, the viability of cells in pH 6.5 group was obviously declined (t=4.412, P<0.05). Compared with that in pH 6.5 group, the viability of cells in pH 6.5+ taxol group was obviously increased (t=2.461, P<0.05). Conclusions: The decline of pH value reduces the viability of cardiomyocytes of rats through destroying the skeleton of microtubule. Stabilizing microtubule skeleton can significantly reduce acidic treatment-induced damage and ameliorate cardiomyocyte viability.

[Evaluation of a high-intensity fluorescent fluorophage method for diagnosis of drug-resistance in tuberculosis]

Objective: To evaluate the high-intensity green fluorescent protein fluorophage Φ(2)GFP10 method for drug susceptibility testing of tuberculosis for isoniazid(INH), rifampin(RIF), and streptomycin(SM). Methods: A total of 128 clinical M. tuberculosis strains were isolated from patients with suspected drug-resistant tuberculosis visiting Beijing Chest Hospital (Beijing, China) from April to June 2014.All of the isolates were tested by the phage assay, while conventional drug susceptibility tests were performing on Lwenstein-Jensen culture medium as reference. Results: The sensitivities of Φ(2)GFP10 assay for INH, RIF, and SM resistance detection were 100.0%, 98.1%(53/54), and 92.6%(50/54), respectively, while their specificities were 84.8%(56/66), 91.9%(68/74), and 91.9%(68/74), respectively. The agreement between the phage assay and the conventional assay for detecting INH, RIF, and SM resistance was 0.92, 0.95 and 0.92, respectively. The Φ(2) GFP10-phage assay could be done within 2 days for RIF and SM, and 3 days for INH. Conclusions: The Φ(2)GFP10-phage method for drug susceptibility test is very sensitive and specific. The method has the potential to be a valuable, rapid and economical screening method for detecting drug-resistant tuberculosis.

Different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease

Celiac disease is associated with the HLA-DR3-DQA1*05:01-DQB1*02:01 and DR4-DQA1*03:01-DQB1*03:02 haplotypes. In addition, there are currently over 40 non-HLA loci associated with celiac disease. This study extends previous analyses on different HLA haplotypes in celiac disease using next generation targeted sequencing. Included were 143 patients with celiac disease and 135 non-celiac disease controls investigated at median 9.8 years (1.4-18.3 years). PCR-based amplification of HLA and sequencing with Illumina MiSeq technology were used for extended sequencing of the HLA class II haplotypes HLA-DRB1, DRB3, DRB4, DRB5, DQA1 and DQB1, respectively. Odds ratios were computed marginally for every allele and haplotype as the ratio of allelic frequency in patients and controls as ratio of exposure rates (RR), when comparing a null reference with equal exposure rates in cases and controls. Among the extended HLA haplotypes, the strongest risk haplotype for celiac disease was shown for DRB3*01:01:02 in linkage with DQA1*05:01-DQB1*02:01 (RR = 6.34; P-value < .0001). In a subpopulation analysis, DRB3*01:01:02-DQA1*05:01-DQB1*02:01 remained the most significant in patients with Scandinavian ethnicity (RR = 4.63; P < .0001) whereas DRB1*07:01:01-DRB4*01:03:01-DQA1*02:01-DQB1*02:02:01 presented the highest risk of celiac disease among non-Scandinavians (RR = 7.94; P = .011). The data also revealed 2 distinct celiac disease risk DR3-DQA1*05:01-DQB*02:01 haplotypes distinguished by either the DRB3*01:01:02 or DRB3*02:02:01 alleles, indicating that different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease. The associated risk of celiac disease for DR3-DRB3*01:01:02-DQA1*05:01-DQB1*02:01 is predominant among patients of Scandinavian ethnicity.

[Dental implantation and soft tissue augmentation after ridge preservation in a molar site: a case report]

For ideal implant rehabilitation, an adequate bone volume, optical implant position, and stable and healthy soft tissue are required. The reduction of alveolar bone and changes in its morphology subsequent to tooth extraction will result in insufficient amount of bone and adversely affect the ability to optimally place dental implants in edentulous sites. Preservation of alveolar bone volume through ridge preservation has been demonstrated to reduce the vertical and horizontal contraction of the alveolar bone crest after tooth extraction and reduce the need for additional bone augmentation procedures during implant placement. In this case, a patient presented with a mandible molar of severe periodontal disease, the tooth was removed as atraumatically as possible and the graft material of Bio-Oss was loosely placed in the alveolar socket without condensation and covered with Bio-Gide to reconstruct the defects of the alveolar ridge. Six months later, there were sufficient height and width of the alveolar ridge for the dental implant, avoiding the need of additional bone augmentation and reducing the complexity and unpredictability of the implant surgery. Soft tissue defects, such as gingival and connective tissue, played crucial roles in long-term implant success. Peri-implant plastic surgery facilitated development of healthy peri-implant structure able to withstand occlusal forces and mucogingival stress. Six months after the implant surgery, the keratinized gingiva was absent in the buccal of the implant and the vestibular groove was a little shallow. The free gingival graft technique was used to solve the vestibulum oris groove supersulcus and the absence of keratinized gingiva around the implant. The deepening of vestibular groove and broadening of keratinized gingiva were conducive to the long-term health and stability of the tissue surrounding the implant. Implant installation and prosthetic restoration showed favorable outcome after six months.

Effects of bedding material composition in deep litter systems on bedding characteristics and growth performance of limousin calves

The objective of this study was to evaluate the effects of different litter mixture compositions on bedding system temperature, pH and volatile fatty acid and ammonia-N (NH₃-N) content, and the serum physico-chemical parameters and growth indices of calves. Thirty-two Limousin calves (280±20 kg) were randomly assigned to four groups (n = 8 for each group) according to the bedding system used: i) control with soil only (CTR); ii) mixture with 50% paddy hulls (PH), 30% saw dusts (SD), 10% peat moss (PM) and 10% corn cobs (CC) (TRT1); iii) mixture with 15% PH, 15% SD, 10% PM, 40% CC, and 20% corn stover (CS) (TRT2); iv) mixture with 30% PH, 10% PM, 40% CC, and 20% CS (TRT3). The litter material combinations of different treatments were based on the cost of bedding system materials in China. The cost of four treatments from low to high: Control<TRT1<TRT2<TRT3. The control was no-cost treatment. The diet consisted of 60.8% silage and 39.2% concentrate (dry matter [DM] basis). The NH₃-N level (271.83 to 894.72 mg/kg) was lowest for TRT1 (p<0.0001) and highest for TRT2 (p<0.0001). The acetate, propionate and butyrate levels were highest for the control group (p<0.0001). In all the groups, the pH value (6.90 to 9.09) increased at the beginning and later remained stable at below 9.09. The temperature of deep litter increased at the first week and reached the maximum (42.1°C) on day 38. 3,5,3′-Triiodothyronine (T₃) levels in the TRT1 group animals (p<0.0001) were lower than those in the control and TRT2 animals. 3,5,3′,5′-Tetraiodothyronine (T₄) in the TRT1 group (p = 0.006) was lower than that in the other treatment groups. Cortisol (COR) in the control and TRT1 group was lower (p<0.0001) than that in the TRT2 and TRT3 groups. Corticosterone (CORt) in the control group was higher (p<0.0001) than that in the treatment groups. The findings indicate that the deep litter bedding systems provided better conditions for animal health and growth performance compared with the control system. Furthermore, the litter composition of TRT1 was found to be optimal among the three treatment groups.

Phase II study of sorafenib in combination with cisplatin and 5-fluorouracil to treat recurrent or metastatic nasopharyngeal carcinoma

BACKGROUND

We aimed to investigate the efficacy and tolerability of sorafenib combined with cisplatin and 5-fluorouracil (5-FU) in patients with recurrent or metastatic nasopharyngeal carcinoma (NPC).

PATIENTS AND METHODS

It was a Simon two-stage designed trial. Chemotherapy-naive patients with recurrent or metastatic disease were enrolled. The regimen was sorafenib 400 mg orally b.i.d., cisplatin 80 mg/m(2) i.v. day 1, and 5-FU 1000 mg/m(2)/day CIV for 4 days, repeated every 21 days. After a maximum of six cycles of chemotherapy, patients received maintenance of sorafenib.

RESULTS

In total, 54 patients were enrolled. The objective response rate reached 77.8%, including 1 complete response and 41 partial responses. The median progression-free survival was 7.2 months (95% CI 6.8-8.4 months), and the median overall survival was 11.8 months (95% CI 10.6-18.7 months). Major toxic effects included hand-foot skin reaction, myelosuppression, and gastrointestinal (GI) reaction. The incidence of hemorrhage was 22.2%, and one patient with liver metastases died of GI bleeding. Contrast-enhanced ultrasonography was carried out in a subset of patients with liver metastases.

CONCLUSION

Combination of sorafenib, cisplatin (80 mg/m(2)) and 5-FU (3000 mg/m(2)) was tolerable and feasible in recurrent or metastatic NPC. Further randomized trials to compare sorafenib plus cisplatin and 5-FU with standard dose of cisplatin plus 5-FU in NPC are warranted.

Patient influx and trauma types in a front-line hospital and a secondary referral hospital after the Wenchuan earthquake: a retrospectively comparative study

PURPOSE

To better understand the differences of patient influx and types of trauma between front-line and referral hospitals after the Wenchuan earthquake, so as to improve the efficiency of injury management.

METHODS

A retrospective and comparative study was performed in Deyang People's Hospital (a front-line hospital) and West China Hospital (a secondary referral hospital).

RESULTS

A total of 1,106 patients were admitted to the front-line hospital, and 1,775 to the secondary referral hospital. The patient flow peaked within 24 h after the quake, and decreased dramatically thereafter in the front-line hospital, while it peaked 2 days after the disaster in the referral one. Extremities were the most frequent location of all identified injuries (48.4% in the front-line hospital and 49.5% in the second-line hospital). Head and trunk injuries were more frequent in the front-line hospital than the referral hospital. Most of the deaths in the front-line hospital occurred within 24 h (6/8), whilst most in the referral hospital died more than 7 days (29/30) after the earthquake. While the total mortality in the front-line hospital was less than that in the referral hospital (0.7 vs 1.7%), the critical mortality in the former was higher (22.8 vs 9.4%).

CONCLUSIONS

There were dramatically different features in terms of quake-related patient influx and types of injury between the epicenter and less-affected hospitals.

Association of SPINK5 gene polymorphisms with atopic dermatitis in Northeast China

BACKGROUND

Defect in the SPINK5 gene is known to be implicated in Netherton syndrome (NS), and has been suggested to be a locus predisposing to atopy in general. Coding polymorphisms in SPINK5 exons 13, 14 and 26 have been reported to be associated with atopic dermatitis (AD), asthma and high level of IgE.

OBJECTIVES

To examine whether the SPINK5 gene polymorphisms are associated with AD in Northeast China, and to assess how variants influence selected phenotypic traits.

METHODS

A case-control study was conducted on four non-synonymous polymorphisms in the coding region of SPINK5 in AD and controls. The SPINK5 gene polymorphisms were analyzed using the PCR and RFLP methods.

RESULTS

For the four non-synonymous SNPs, A1103G(Asn368Ser), G1156A(Asp386Asn), G1258A(Glu420Lys), G2475T(Glu825Asp) in SPINK5, the allelic frequencies in the AD cohort were 0.55 for 1103G, 0.57 for 1156A, 0.54for 1258A, 0.62 for 2475T, consistent with those already published in the original British and Japanese cohorts. The T allele of SNP 2475G > T was found to be significantly associated with AD. There were significant differences in genotype frequencies for G1258A(Glu420Lys) and G2475T(Glu825Asp) but not for A1103G(Asn368Ser) and G1156A(Asp386Asn). Genotypes GA(420Glu/Lys), TT (2475Asp/Asp) and GT(2475Glu/Asp) were significantly more frequent in AD. However, the SPINK5 gene polymorphisms was found not to be associated with AD in regard to either serum IgE levels, concurrent allergic asthma or early onset of AD.

CONCLUSIONS

Our study confirms the association between SPINK5 and AD.

Genetic variation in CXCL12 and risk of cervical carcinoma: a population-based case-control study

CXCL12 provides a chemotactic signal-directing leucocyte migration and regulates metastatic behaviour of tumour cells. We conducted a population-based case-control study to test the hypothesis that common genetic variation in CXCL12 individual single nucleotide polymorphism (SNP) alleles and haplotypes] is associated with the risk of cervical carcinoma. Cases (n = 917) were residents of western Washington State diagnosed with invasive squamous cell cervical carcinoma (SCC), invasive adenocarcinoma or adenosquamous carcinoma, or adenocarcinoma in situ of the cervix. Control participants (n = 849) were identified from the source population by random digit telephone dialling and frequency matched to cases on county and age. Nine CXCL12 tagSNPs chosen from the SeattleSNPs database were genotyped. The minor allele of intronic SNP rs266085 was inversely associated with cervical cancer under a recessive genetic effects model (OR = 0.74, 95% CI: 0.56-0.98). Among the ten common haplotypes inferred from the nine tagSNPs, one haplotype defined by minor alleles at 5'-flanking SNP rs17885289 and rs266085, and common alleles at the other seven SNPs occurred among 7.8% of cases and 10.6% of controls (dominant model OR = 0.72, 95% CI: 0.56-0.93; recessive model OR = 0.35, 95% CI: 0.12-0.97; and log-additive model OR = 0.72, 95% CI: 0.57-0.90). A stepwise procedure identified rs17885289, rs266085 and 3'-untranslated region (UTR) SNP rs266093 as the most parsimonious subset of SNPs necessary to define the haplotype inversely associated with cervical cancer risk in our study. A 3'-UTR SNP, rs1801157, previously found to be related to HIV pathogenesis, was not associated with cervical cancer risk. Further population-based studies are warranted to confirm these associations between genetic variation in CXCL12 and cervical cancer risk.

Improving the system stability of a digital Shack-Hartmann wavefront sensor with a special lenslet array

There has been very limited study on the stability of a Shack-Hartmann wavefront sensor (SHWS) since its emergence in the early 1970s. In this paper, through experimental study of the system stability of a digital SHWS, a special lenslet array with long focal range is designed and implemented with a spatial light modulator to improve the system performance. Diffractive lenses with long focal length range can provide pseudo-nondiffracting beams and a long range of focusing plane. The performance and effect of the modified SHWS with this lenslet array are investigated, and the experimental results show that the system stability and measurement repeatability are not sensitive to the sensing distance and stay at an acceptable level.

Asymmetrical optical lenslet array realized by spatial light modulator for measuring toroidal surfaces

The Shack-Hartmann wavefront sensor (SHWS) recently has been extensively researched for optical surface metrology due to its extendable dynamic range compared with interferometry technique. In this paper, we proposed to use a digital SHWS to measure toroidal surfaces, which are widely used in many optical systems due to their different symmetries and curvatures in the X and Y directions. For what is believed to be the first time, an asymmetrical optical lenslet array implemented by a spatial light modulator was presented to tackle the measurement challenge. This unconventional design approach has a great advantage to provide different optical powers in the X and Y directions so that focusing spots can be formed and captured on the detector plane for accurate centroid finding and precise wavefront evaluation for 3D shape reconstruction of the toroidal surface. A digital SHWS system with this extraordinary microlens array was built to verify the design concept, and the experimental results were presented and analyzed.

Resequencing of the human major histocompatibility complex in patients with rheumatoid arthritis and healthy controls in Alaska Natives of Southeast Alaska

High prevalence and severity of rheumatoid arthritis (RA) with an early age of onset have previously been described in Alaska Native and American Indian (AN/AI) populations. The contribution of HLA-DRB1 alleles encoding a similar amino acid sequence, referred to as the shared epitope (SE), to RA risk is well recognized in multiple populations worldwide. DRB1*1402 allele is the major SE-encoding allele in AN/AI populations. However, DRB1*1402 is highly prevalent in healthy Alaska Natives of Southeast Alaska (AN), with no significant difference from RA patients, indicating this allele alone is not informative for defining genetic risk and non-human leukocyte antigen (non-HLA) genes are likely important in AN. We sought to deep resequence the human major histocompatibility complex (MHC) to characterize the single-nucleotide polymorphism (SNP) haplotypes within this region in RA cases and controls in AN. Approximately 99 kb of the MHC was resequenced with 95 amplicons throughout this region. Thirty-four cases and 74 controls were examined. A total of 696 SNPs were discovered from 85 of the selected 95 amplicons. Disease association signals were detected for nine of the 95 amplicons analyzed. Increased risk of RA was associated with five amplicons in the class I, class II or class III region and resistance to disease with four amplicons in the class I region. Our results indicate that non-HLA MHC genes and/or unknown exogenous factors likely modulate risk of RA in the AN population.

SignalViewer: analyzing microarray images

Microarray technology is now routinely used to monitor genome-wide expression profiles. However, current microarray imaging and analysis packages typically require manual intervention and assumptions on alignments. Unfortunately, limitations and assumptions are typically undisclosed and methods are not published. To facilitate exploration of image data, we developed SignalViewer. This paper presents a description of the application.

A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays

The increasing use of cDNA microarrays necessitates the development of methods for extracting quality data. Here, we set forth hurdles to overcome in image analysis of microarrays. We emphasize the importance of objective data extraction methods resulting in reliable signal estimates. Based on statistical principles, we describe a method for automated grid alignment, spot detection, background estimation, flagging, and signal extraction. A software application that we call SignalViewer has been implemented for this method. We identify areas where we improved upon current methods used for array image analysis at each step in the process. Finally, we give examples to illustrate the performance of our algorithms on raw data.

Incorporating age at onset information into the transmission/disequilibrium test

In this paper, we proposed two approaches for incorporating the age at onset into the transmission/disequilibrium test (TDT). Trios (affected offspring and their parents) were extracted from the first four replicate data sets of the general population type. Focusing on chromosome 6 where MG6 and MG7 reside, we compared the usual TDT with the newly proposed tests in terms of gene localization.

An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.

Statistical modeling of large microarray data sets to identify stimulus-response profiles

A statistical modeling approach is proposed for use in searching large microarray data sets for genes that have a transcriptional response to a stimulus. The approach is unrestricted with respect to the timing, magnitude or duration of the response, or the overall abundance of the transcript. The statistical model makes an accommodation for systematic heterogeneity in expression levels. Corresponding data analyses provide gene-specific information, and the approach provides a means for evaluating the statistical significance of such information. To illustrate this strategy we have derived a model to depict the profile expected for a periodically transcribed gene and used it to look for budding yeast transcripts that adhere to this profile. Using objective criteria, this method identifies 81% of the known periodic transcripts and 1,088 genes, which show significant periodicity in at least one of the three data sets analyzed. However, only one-quarter of these genes show significant oscillations in at least two data sets and can be classified as periodic with high confidence. The method provides estimates of the mean activation and deactivation times, induced and basal expression levels, and statistical measures of the precision of these estimates for each periodic transcript.

Integrated designs for gene discovery and characterization

Recent advances, including near completion of the human genome map, ever improving high-throughput technologies, and successes in discovering chronic disease-related genes, have stimulated the further development of genetic epidemiology. The primary mission of genetic epidemiology is to discover and characterize genes, whether independent of or interactive with environmental factors, that cause human diseases. To accomplish such a mission, genetic epidemiology needs to integrate both genetic and epidemiologic approaches. One of the challenges facing such an integrated approach is the identification of study designs that are efficient for both gene discovery and characterization. Because designs for gene discovery alone and designs for gene characterization alone have been elaborated in the other two panels, the focus of this paper is to describe those designs that may be useful for discovery and characterization jointly, including case-family and case-control-family designs. Examples of integrated designs are described, and studies of breast cancer conducted at the Fred Hutchinson Cancer Research Center are used for illustration. Finally, related analytic issues are also discussed.

Population-based family study designs: an interdisciplinary research framework for genetic epidemiology

Most complex traits such as cancer and coronary heart diseases are attributed either to heritable factors or to environmental factors or to both. Dissecting the genetic and environmental etiology of complex traits thus requires an interdisciplinary research strategy. Genetic studies generally involve families and investigate familial aggregations of traits, segregation of major disease genes, and locations of disease genes on the human genome, the latter of which can be identified via linkage analysis. Epidemiologic studies often use population-based case-control studies to establish the role of specific environmental factors. Integrating both objectives, genetic epidemiology is to assess the associations of environmental factors with disease status, to quantify the aggregation of cases within families, to characterize putative disease genes via segregation analysis, and to localize disease genes via linkage analysis with genetic markers. To accomplish these objectives through designed studies, we propose a class of population-based family study designs, which are formed by choosing among sampling designs at three stages. The objectives of sampling at these three stages are 1) combined aggregation and association analysis, 2) combined segregation, aggregation, and association analysis, and 3) combined linkage, segregation, aggregation, and association analysis. These designs form an interdisciplinary research framework for genetic epidemiology. Our preliminary exploration of this framework and related analytic methods indicates that population-based family study designs retain the efficiency of linkage analysis for localizing disease genes without losing the property of being population-based, and they will therefore allow an assessment of a joint contribution of genetic and environmental factors to complex traits.

A population-based family study (II): Segregation analysis

We used segregation analysis to investigate the genetic etiology of the disease in Problem 2A. Under the assumption of a dominant major gene, our analysis suggests a major gene with relative risk of 58 and an allele frequency of 0.013. Under an additive gene assumption, it appears that there may be two genes with relative risks of 39 and 17 and allele frequencies of 0.015 and 0.075, respectively.

A note on a conditional-likelihood approach for family-based association studies of candidate genes

The family-based association study design is a variation of the case-control study design, where unaffected family members instead of unrelated subjects are sampled as controls. This variation is useful in assessing the effects of candidate genes on disease, because it avoids false associations caused by admixture of populations. A complication of this design is that because of an inherited genotypic correlation among family members, the genotypic distributions between cases and relative controls may be distorted by the ascertainment criteria of families, which could involve not only cases and relative controls, but also other relatives. Analyzing such data naively may lead to biased estimates of relative risk. In this note, we will discuss the consistency of a conditional-likelihood approach. We show analytically that maximum conditional-likelihood estimators are consistent for the true relative risks, if genotypes for family members are exchangeable under the sampling process, for example, sibling clusters. Besides being straightforward conceptually and computationally, this approach is robust to ascertainment bias and naturally accommodates genetic heterogeneity across families.

Assessing changes in ages at onset over successive generation: an application to breast cancer

Decreased age at onset in successive generations has been observed for a number of diseases. Two nonparametric matched and unmatched test statistics are proposed, taking into account not only current age or age at death for unaffected individuals and age at disease onset for affected individuals, but also possible correlations among family members. Both are asymptotically normal with readily estimated variances from the data. A simulation study is conducted to compare the proposed tests with the commonly used paired t-test and log-rank test. It has been shown that the proposed test statistics yield valid conclusions in assessing genetic anticipation under all situations considered. However, the paired t-test is valid only when the censoring distributions are comparable between two generations, whereas the log-rank test is valid when the correlation among family members is weak. As expected, the matched test is most powerful when the data are heterogeneous, and the unmatched and the log-rank tests are most powerful when the data are homogeneous and the correlation is weak. Lastly, a population-based family study of breast cancer conducted at the Fred Hutchinson Cancer Research Center is used for illustration of the proposed and the log-rank tests. The preliminary analysis suggests that there appears a decreased age at onset over the successive generations in breast cancer.

Mapping alcoholism genes using linkage/linkage disequilibrium analysis

Using a recently developed semiparametric method for combined linkage/linkage-disequilibrium analysis, we analyzed the Collaborative Study on the Genetics of Alcoholism data subset developed for Genetic Analysis Workshop 11 (GAW11). This semiparametric approach estimates recombination fractions for linkage, marker log odds ratios for linkage-disequilibrium, their product for combined linkage/linkage-disequilibrium, and corresponding z-scores. We used two outcomes: alcohol dependence and "alcoholism-free" and a genome-wide significance level of 4.1 (which corresponds to a genome-wide lod score of 3.6). For the alcohol dependence outcome, we observed significant linkage signals at D1S1588-D1S1631, D1S547, D2S399, D2S425, D4S2361, D7S1796, and D7S1824. We also found significant linkage-disequilibrium signals at D1S547 and D7S1795. For the "alcoholism-free" outcome, we found significant linkage signals at D4S2457, D41651 (both flank ADH3), D11S2359, and D16S47 and significant linkage-disequilibrium signals at D4S2361, FABP2, D11S2359, D19S431 and D19S47-D19S198-D19S601.

A genome-wide scan for a simulated data set using two newly developed methods

A genome-wide scan of a simulated data set for fictitious disease genes was conducted using both semiparametric and nonparametric methods. The semiparametric model-based method, which tests for linkage/linkage disequilibrium separately and together, correctly identified all three underlying disease loci along with two false positives through the linkage analysis. However, the nonparametric model-free method which tests combined linkage/linkage disequilibrium, failed to yield any results due to the lack of linkage disequilibrium information in the data.

An efficient protocol for rare mutation genotyping in a large population

We introduce a method to efficiently detect rare mutations for individual subjects in a large population by pooling samples and retesting subgroups of positive pooled samples. We conducted computer simulations of this method and discovered that it seems efficient for mutation prevalences less than 0.1, regardless of the number of samples. The simulations also indicate that splitting the pooled samples into three to five subgroups at each level is optimal. The expected number of necessary tests and relative efficiency of this method are given, by mutation prevalence and sample size.

An efficient, robust and unified method for mapping complex traits (III): combined linkage/linkage-disequilibrium analysis

Extending the method for linkage analysis [Zhao et al., 1998a: Am. J. Med. Genet. 77:366-383; 1998b: Am. J. Med. Genet. 79:49-61], this article describes a method for the linkage-disequilibrium analysis, and for combining linkage and linkage-disequilibrium analyses. As highly dense markers are increasingly used in genome scans, one or more markers are not only linked with the disease genes if they exist, but also likely in linkage-disequilibrium with those putative genes. Hence, linkage-disequilibrium analysis potentially offers additional information about positions of putative disease genes. Combining both linkage and linkage-disequilibrium signals, this approach is able to improve positional signals. As before, the proposed method is a model-based approach, but semiparametric via the estimating equation technique. Under the assumptions of penetrance and allele frequency, this method efficiently estimates recombination fractions for linkage analysis and odds ratios for linkage-disequilibrium analysis. As described in two previous papers, this method is relatively more robust than the lod score methods, since it requires weaker assumption than conditional independence. While the estimated recombination fractions are used for inference as part of linkage analysis, the estimated odds ratios are used for linkage-disequilibrium inference and combined linkage, and linkage-disequilibrium parameters can be used to test combined linkage/linkage-disequilibrium analysis. This approach has been implemented, named gSCAN, and its compiled version is available for trial on request via the web site (http:/lynx.fhcrc.org/qge). We applied this new approach to affected sib-pair data collected for the genome scan to localize type 1 diabetes genes. Under an assumed autosomal dominant gene model, the linkage analysis confirms an earlier suggestion of one major gene around D6S281. Interestingly, the linkage-disequilibrium analysis suggests several additional signals around D6S250, GATA30, D6S311, D6S441, D6S442, D6S415, D6S411, D6S305, and a290xh9. The linkage analysis, on the other hand, suggests a signal around D6S281, while providing supporting evidence for several other marker loci. However, the combined analysis did not provide strong support for any of the findings, implying that linkage and linkage-disequilibrium findings are not consistent.

On the assessment of statistical significance in disease-gene discovery

One of the major challenges facing genome-scan studies to discover disease genes is the assessment of the genomewide significance. The assessment becomes particularly challenging if the scan involves a large number of markers collected from a relatively small number of meioses. Typically, this assessment has two objectives: to assess genomewide significance under the null hypothesis of no linkage and to evaluate true-positive and false-positive prediction error rates under alternative hypotheses. The distinction between these goals allows one to formulate the problem in the well-established paradigm of statistical hypothesis testing. Within this paradigm, we evaluate the traditional criterion of LOD score 3.0 and a recent suggestion of LOD score 3.6, using the Monte Carlo simulation method. The Monte Carlo experiments show that the type I error varies with the chromosome length, with the number of markers, and also with sample sizes. For a typical setup with 50 informative meioses on 50 markers uniformly distributed on a chromosome of average length (i.e., 150 cM), the use of LOD score 3.0 entails an estimated chromosomewide type I error rate of.00574, leading to a genomewide significance level >.05. In contrast, the corresponding type I error for LOD score 3.6 is.00191, giving a genomewide significance level of slightly <.05. However, with a larger sample size and a shorter chromosome, a LOD score between 3.0 and 3.6 may be preferred, on the basis of proximity to the targeted type I error. In terms of reliability, these two LOD-score criteria appear not to have appreciable differences. These simulation experiments also identified factors that influence power and reliability, shedding light on the design of genome-scan studies.

An efficient, robust, and unified method for mapping complex traits (II): multipoint linkage analysis

Extending the method for two-point linkage analysis [Zhao et al., 1998: Am J Med Genet 77:366-383], this paper introduces a semiparametric method for multipoint linkage analysis, expected to gain efficiency by using multiple markers simultaneously. Overcoming the longstanding statistical and computational challenge to the parametric approaches (or lod score methods) for multipoint linkage analysis, this semiparametric approach, based on the estimating equation technique, yields statistically efficient and yet robust estimates and enjoys the computational efficiency in processing multiple markers from large pedigrees. Its computational burden increases linearly with the sizes of pedigrees and with the number of marker loci. To illustrate this semiparametric method, we apply it to marker data gathered for the Breast Cancer Consortium. The result supports the earlier finding of the positive linkage with BRCA1 and has also shown that the multipoint linkage analysis has an improved power. In addition, we have applied this method to analyze genome scanning data that have been used to localize genes responsible for type 1 diabetes. In support of the earlier findings, the genome scanning detects the linkage signals on chromosome 6 but does not support the earlier suggestions of two major genes in that genome segment. Through sensitivity analysis, it appears that the results are robust to misspecification of penetrance and allele frequency.

Embryonic cardiomyocyte hypoplasia and craniofacial defects in G alpha q/G alpha 11-mutant mice

Heterotrimeric G proteins of the Gq class have been implicated in signaling pathways regulating cardiac growth under physiological and pathological conditions. Knockout mice carrying inactivating mutations in both of the widely expressed G alpha q class genes, G alpha q and G alpha 11, demonstrate that at least two active alleles of these genes are required for extrauterine life. Mice carrying only one intact allele [G alpha q(-/+);G alpha 11(-/-) or G alpha q(-/-);G alpha 11(-/+)] died shortly after birth. These mutants showed a high incidence of cardiac malformation. In addition, G alpha q(-/-);G alpha 11(-/+) newborns suffered from craniofacial defects. Mice lacking both G alpha q and G alpha 11 [G alpha q(-/-);G alpha 11(-/-)] died at embryonic day 11 due to cardiomyocyte hypoplasia. These data demonstrate overlap in G alpha q and G alpha 11 gene functions and indicate that the Gq class of G proteins plays a crucial role in cardiac growth and development.

Mapping of complex traits by single-nucleotide polymorphisms

Molecular geneticists are developing the third-generation human genome map with single-nucleotide polymorphisms (SNPs), which can be assayed via chip-based microarrays. One use of these SNP markers is the ability to locate loci that may be responsible for complex traits, via linkage/linkage-disequilibrium analysis. In this communication, we describe a semiparametric method for combined linkage/linkage-disequilibrium analysis using SNP markers. Asymptotic results are obtained for the estimated parameters, and the finite-sample properties are evaluated via a simulation study. We also applied this technique to a simulated genome-scan experiment for mapping a complex trait with two major genes. This experiment shows that separate linkage and linkage-disequilibrium analyses correctly detected the signals of both major genes; but the rates of false-positive signals seem high. When linkage and linkage-disequilibrium signals were combined, the analysis yielded much stronger and clearer signals for the presence of two major genes than did two separate analyses.

Efficient, robust, and unified method for mapping complex traits (I): two-point linkage analysis

The completion of a preliminary human genome map and development of molecular methods have enabled researchers to assay a large number of polymorphic markers that are evenly spaced along the entire human genome. Among many applications, marker data are valuable for mapping complex traits through linkage or linkage-disequilibrium analysis, the former of which is the focus of this paper, the first in a series on this subject. Formalizing the concept and computation for linkage analysis, Elston and Stewart [1971; Human Heredity 21:523-542] introduced a likelihood function to capture relevant genetic information and a recursive algorithm for computing the likelihood function. However, the computing burden is prohibitive in processing complex pedigrees. Since that fundamental development, improving the computational algorithm and extending the method has been a dynamic area of research. The primary objective of this communication is to introduce a semiparametric method for linkage analysis. It is a particularly suitable approach with desirable properties for mapping complex traits that may be binary, continuous, and partially observed (i.e., censored). It incorporates candidate genes, environmental factors, and their interactions with the putative gene and is expected to be robust and efficient in comparison with likelihood-based methods. The properties of the estimates have been studied in finite samples with a limited simulation study. This method is illustrated with an application to family data contributed to the Breast Cancer Consortium.

Family history and risk of colorectal cancer in the multiethnic population of Hawaii

Increased risk of colorectal cancer in individuals with family history of the disease has been observed consistently in past studies. However, limited attention has been given to the influence of ethnicity, the characteristics of the proband's tumor, and kinship. A population-based case-control study was conducted between 1987 and 1991 in Hawaii among 1,192 incident colorectal cancer cases and 1,192 sex-, age-, and ethnicity-matched population controls. The study identified 7,673 relatives for the cases and 7,823 relatives for the controls. With an estimating equation-based regression method, relatives of cases were found to have a 2.5-fold increased risk of colorectal cancer compared with relatives of controls (95% confidence interval (CI) 1.8-3.4) after adjustment for covariates. This increase in risk was greater for Japanese (odds ratio (OR) = 3.0, 95% CI 1.7-5.4) than Caucasians (OR = 1.8, 95% CI 1.2-2.9), for siblings (OR = 3.1, 95% CI 2.1-4.6) than parents (OR = 2.0, 95% CI 1.1-3.1), and when the index patient was diagnosed before the age of 55 years (OR = 4.1, 95% CI 2.1-8.0) with multiple tumors (OR = 9.5, 95% CI 4.4-20.6), with a distant stage (OR = 4.6, 95% CI 2.7-7.8), or with cancer of the right colon (OR = 3.0, 95% CI 2.0-4.4) or the rectum (OR = 3.0, 95% CI 1.8-4.8). The increase in risk was not affected by the relative's sex. Relatives of cases were not at increased risk for other common cancers. It is estimated that approximately 11.1% and 6.5% of colorectal cancers are attributable to a first degree family history of the disease for Japanese and Caucasians, respectively. These data and those of previous studies strongly suggest that individuals with a family history of colorectal cancer in a first degree relative are at increased risk for the disease and should receive regular diagnostic screening. Characteristics of the index case, such as age and stage at diagnosis, subsite and number of tumors, and race, as well as kinship, may be important in assessing the colorectal cancer risk of a relative.

Regression analysis with missing covariate data using estimating equations

In regression analysis, missing covariate data has been among the most common problems. Frequently, practitioners adopt the so-called complete-case analysis, i.e., performing the analysis on only a complete dataset after excluding records with missing covariates. Performing a complete-case analysis is convenient with existing statistical packages, but it may be inefficient since the observed outcomes and covariates on those records with missing covariates are not used. It can even give misleading statistical inference if missing is not completely at random. This paper introduces a joint estimating equation (JEE) for regression analysis in the presence of missing observations on one covariate, which may be thought of as a method in a general framework for the missing covariate data problem proposed by Robins, Rotnitzky, and Zhao (1994, Journal of the American Statistical Association 89, 846-866). A generalization of JEE to more than one such covariate is discussed. The JEE is generally applicable to estimating regression coefficients from a regression model, including linear and logistic regression. Provided that the missing covariate data is either missing completely at random or missing at random (in addition to mild regularity conditions), estimates of regression coefficients from the JEE are consistent and have an asymptotic normal distribution. Simulation results show that the asymptotic distribution of estimated coefficients performs well in finite samples. Also shown through the simulation study is that the validity of JEE estimates depends on the correct specification of the probability function that characterizes the missing mechanism, suggesting a need for further research on how to robustify the estimation from making this nuisance assumption. Finally, the JEE is illustrated with an application from a case-control study of diet and thyroid cancer.

Cloning and characterization of myr 6, an unconventional myosin of the dilute/myosin-V family

We have isolated cDNAs encoding a second member of the dilute (myosin-V) unconventional myosin family in vertebrates, myr 6 (myosin from rat 6). Expression of myr 6 transcripts in the brain is much more limited than is the expression of dilute, with highest levels observed in choroid plexus and components of the limbic system. We have mapped the myr 6 locus to mouse chromosome 18 using an interspecific backcross. The 3' portion of the myr 6 cDNA sequence from rat is nearly identical to that of a previously published putative glutamic acid decarboxylase from mouse [Huang, W.M., Reed-Fourquet, L., Wu, E. & Wu, J.Y. (1990) Proc. Natl. Acad. Sci. USA 87, 8491-8495].

Estimating relative risk functions in case-control studies using a nonparametric logistic regression

The authors describe an approach to the analysis of case-control studies in which the exposure variables are continuous, i.e., quantitative variables, and one wishes neither to categorize levels of the exposure variable nor to assume a log-linear relation between level of exposure and disease risk. A dose-response association of an exposure variable with a disease outcome can be depicted by estimated relative risks at various exposure levels, and the functional relation between exposure dose and disease risk is here termed a relative risk function (RRF). A RRF takes values that are greater than zero: Values less than one imply lower risk; the value one implies no risk, and values greater than one imply increased risk, when compared with a reference value. The authors describe how a nonparametric logistic regression can be used to estimate and display these RRFs. Using data from a previously published case-control study of diet and colon cancer, RRFs for total energy, dietary fiber, and alcohol intakes are compared with the original results obtained from using categorized levels of exposure variables. For total energy and alcohol intakes, there were meaningful differences in study results based on the two analytic approaches. For energy, the nonparametric logistic regression detected a significant protective effect of low intakes, which was not found in the original analysis. For alcohol, the nonparametric logistic regression suggested that there were two underlying populations, non- or very light drinkers and moderate to heavy drinkers, with different relation of dose to disease risk. In contrast, the original analysis found a nonlinear increase in risk across intake categories and did not detect the complex, bimodal nature of the exposure distribution. These results demonstrate that nonparametric logistic regression can be a useful approach to displaying and interpreting results of case-control studies.

Assessing familial aggregation of age at onset, by using estimating equations, with application to breast cancer

In genetic research of chronic diseases, age-at-onset outcomes within families are often correlated. The nature of correlation of age-at-onset outcomes is indicative of common genetic and/or shared environmental risk factors among family members. Understanding patterns of such correlation may shed light on the disease etiology and, hence, is an important step to take prior to further searching for the responsible genes via segregation and linkage studies. Age-at-onset outcomes are different from those familiar quantitative or qualitative traits for which many statistical methods have been developed. In comparison with the quantitative traits, age-at-onset outcomes are often censored, i.e., instead of actual age-at-onset outcomes, only the current ages or ages at death are observed. They are also different from qualitative traits because of their continuity. Because of the complexity of correlated censored outcomes, few methods have yet been developed. A traditional approach is to impose a parametric joint distribution for the correlated age-at-onset outcomes, which has been criticized for requiring a stringent assumption about the entire distribution of age at onset. The purpose of this paper is to describe a method for assessing familial aggregation of correlated age-at-onset outcomes semiparametrically, by use of estimating equations. This method does not require any parametric assumption for modeling the age at onset. The estimates of parameters, including those quantifying the correlation within families, are consistent and have an asymptotic normal distribution that can be used to make inferences. To illustrate this new method, we analyzed two age-at-onset data sets that were obtained from studies conducted in the States of Washington and Hawaii, with the objective of quantifying the familial aggregations of age at onset of breast cancer.