Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent-the probability that different Alu elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 ± 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.The Alu family of short interspersed elements is one of the most successful mobile genetic elements, having arisen to a copy number in excess of 500,000 within primate genomes in the last 65 million years (for recent reviews, see Okada 1991;Schmid and Maraia 1992; Batzer 1993, 1995). Alu repeats are thought to be ancestrally derived from the 7SL RNA gene and mobilize through an RNA polymerase III-derived transcript in a process termed retroposition. Each Alu sequence is ∼300bp in length; therefore, Alu repeats comprise ∼5% of the human genome.Alu sequences can be divided into different subfamilies or clades of related elements based on commonly shared diagnostic mutations. Here, we use the new standardized nomenclature to refer to various Alu subfamilies (Batzer et al. 1996a). Two of the most recently formed subfamilies of Alu elements within the human genome have been termed Ya5 and Ya8 (Batzer et al. 1990;. Members of the Ya8 Alu subfamily are characterized by all five of the Ya5 diagnostic mutations, as well as three additional diagnostic mutations. Be- GENOME RESEARCH 1061Cold Spring Harbor Laboratory Press on May 12, 2018 -Published by genome.cshlp.org Downloaded from cause both the Ya5 and Ya8 Alu subfamilies share a number of diagnostic mutations we refer to this lineage collectively as Ya5/8 (Batzer et al. 1996b). The Ya5/8 Alu subfamily lineage is comprised of 500-2000 elements that are restricted to the human genome (Arco...

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In this work, we study the influence of in-plane and through-plane fiber orientations on a fibrous medium’s transverse permeability. Three-dimensional virtual geometries resembling the microstructure of fibrous media with different fiber orientations are developed to be utilized in permeability calculations conducted by numerically solving the Stokes equations in the void space between fibers. Results of our simulations are compared to existing experimental and analytical studies from literature and excellent agreement is observed. We, in particular, demonstrate that the transverse permeability of a fibrous medium is independent of in-plane fiber orientation but increases with increasing deviation of the fibers’ through-plane angle from zero. Our findings somewhat disagree with some of the conclusions made by Stylianopoulos et al. [Phys. Fluids 20, 123601 (2008)].

Aim:  To estimate the incidence of musculoskeletal pain and rheumatic disorders in a Bangladeshi rural community. Methods:  This study was conducted in six villages near Dhaka from January 2001 to June 2002. Door‐to‐door case finding by interviewers was followed by interviewing and examination of positive respondents by trained doctors. The respondents with inflammatory arthropathies were reviewed 5 years later, in December 2006. Results:  Four hundred and forty‐one (M = 163, F = 278) out of 2685 adults (M = 1324, F = 1361) developed new musculoskeletal pain yielding an incidence rates of 10.9/100 person‐years (PY) (M = 8.2, F = 13.6). The incidence was highest in the 35–44‐year age group in both genders. It was highest in housewives, followed by weavers and cultivators. The spine (7.5/100 PY) was the most common affected part followed by knees (6.5), shoulder (6.2) and neck (6.2). The most common cause of new musculoskeletal pain was non‐specific low back pain, followed by fibromyalgia and knee osteoarthritis. Forty‐one subjects (M = 17, F = 24) developed inflammatory joint or spinal pain (1000/100,000 PY). The incidence of rheumatoid arthritis, combined spondyloarthropothies, ankylosing spondylitis, reactive arthropathy and psoriatic arthritis were 120 (M = 101, F = 147), 150 (M = 252, F = 49), 75 (M = 151, F = 0), 50 (M = 101, F = 0) and 25 (M = 0, F = 49) per 100,000 PY, respectively. Thirty‐one cases had undiagnosed arthropathies (770/100,000 PY). Seven were unavailable in December, 2006 and one died. The remaining 23 were symptom‐free. Conclusions:  The incidence of musculoskeletal pain and rheumatic disorders is considerable in this Bangladeshi rural community. Common incident disorders are non‐specific low back pain, fibromyalgia and osteoarthritis of knees. Inflammatory arthropathies are not common. The majority of undiagnosed arthopathies undergo spontaneous lasting remission.

This study was performed to assess the feasibility and accuracy of ultrasound guided fine needle aspiration biopsy for axillary staging in invasive breast cancer. Data were collected prospectively from June 2005 to June 2006. In all, 197 patients with invasive breast cancer and clinically nonsuspicious axillary lymph nodes were included. Patients with suspicious nodes on ultrasound had fine needle aspiration biopsy. Those with fine needle aspiration biopsy positive for malignancy were planned for axillary nodes clearance otherwise they had sentinel node biopsy. Patients (41) had ultrasound guided fine needle aspiration biopsy. Three cases were excluded for being nonconclusive. Postoperative histology showed 18/38 cases (47.4%) axillary lymph nodes positive and 20/38 cases (52.6%) axillary nodes negative. Ultrasound guided fine needle aspiration biopsy was positive in 8/38 cases (21.1%), negative in 30/38 cases (78.9%). The sensitivity of ultrasound guided fine needle aspiration biopsy was found to be 47.1%, specificity 100%, positive predictability 100%, negative predictability 70%, and overall accuracy 76.3%. Ultrasound guided fine needle aspiration biopsy was found to be more accurate and sensitive when two or more nodes were involved, raising the sensitivity to 80% and negative predictability to 93.3%. Preoperative axillary staging with ultrasound guided fine needle aspiration biopsy in invasive breast cancer patients is very beneficial in diagnosing nodes positive cases. These cases can be planned for axillary lymph nodes clearance straightaway therefore saving patients from undergoing further surgery as well as time and resources.

Radiation induced angiosarcomas (RIA) can affect breast cancer patients who had radiotherapy following conservative breast surgery. They are very rare tumors and often their diagnosis is delayed due to their benign appearance and difficulty in differentiation from radiation induced skin changes. Therefore it is very important that clinicians are aware of their existence. We report here a case of RIA followed by discussion and review of literature.

We present a case of a giant inguinoscrotal hernia reaching up to the patient's knees. It was only partially reducible but was not associated with any other complications. It was treated by an inguinal incision and the reduction of contents aided by a small midline infra-umbilical incision. The hernial sac contained loops of small bowel along with its mesentery, appendix, cecum and ascending colon. The defect was repaired using prolene mesh.

In this study, we evaluated the diagnostic accuracy and cost-effectiveness of ascitic fluid interferon-gamma (IFN-gamma) and adenosine deaminase (ADA) assays in the diagnosis of tuberculous ascites. Ascitic fluid from patients with proven tuberculosis (TB) (n = 31) and non-TB ascites (n = 88) was analyzed for IFN-gamma and ADA levels. Areas under the receiver operative characteristic (ROC) curves (AUCs) for the two biologic markers were compared. Levels of ascitic fluid IFN-gamma, median (range): 560 (104-1600) pg/mL vs. 4.85 (0-320) pg/mL (p < 0.001), and ADA, median (range): 58 (16-331) IU/L vs. 10 (0-59) IU/L (p = 0.001), were significantly different between TB and non-TB groups. IFN-gamma and ADA assays showed equal sensitivity (0.97) and differed marginally in specificity (0.97 vs. 0.94). Difference in AUCs was not significant (0.99 vs. 0.98, p < 0.62). For differentiating TB from non-TB ascites, optimal cutoff points were 112 pg/mL for IFN-gamma and 37 IU/L for ADA. The accuracy of the ADA assay was similar to that of the IFN-gamma assay in differentiating of TB from non-TB ascites. Because both material and human costs of the ADA assay are far less than those of the IFN-gamma assay, the former is probably the most appropriate diagnostic test for analysis of peritoneal fluid in resource- limited settings.