bluuebunny/crossref_metadata_2025_split huggingface dataset:
Picking transplant glomerulopathy out of the CAN: evidence from a clinico-pathological evaluation
Authors: Sun Qiquan , Huang Xianghua , Jiang Song , Zeng Caihong , Liu Zhihong 
Published: September 2012

Abstract

Background
Since the term chronic allograft nephropathy (CAN) was removed from the Banff scheme in 2005, transplant glomerulopathy (TG) has been regarded as a clinicopathological entity that is one of the major causes of graft loss. To assess the distinction between CAN and TG, we performed a comprehensive evaluation comparing TG with traditional CAN.

Methods
We compared the clinicopathological features of 43 cases of TG with 43 matched cases of non-TG CAN (non-TG group) after renal transplantation. TG was diagnosed by light microscopy based on the double contours of the glomerular basement membranes, and the Banff 97 classification system was used to score TG severity (cg0-3).

Results
Compared to the control group, we found a significantly higher incidence of positivity for human leukocyte antigen class-I and II antibodies, a higher incidence of hepatitis C virus (HCV) infection, and poorer graft survival in TG patients. Clinically, TG was associated with a higher prevalence of proteinuria, hematuria, anaemia and hypoalbuminemia. Histologically, TG strongly correlated with antibody related microcirculatory injuries, including glomerulitis, peritubular capillaritis and peritubular capillary (PTC) C4d deposition. Interestingly, the TG patients showed a significantly higher incidence of IgA deposition than the control patients. C4d-positive TG was correlated with higher TG and PTC scores, and PTC C4d deposition was correlated with a more rapid progression to graft dysfunction. TG accompanied by HCV infection was associated with heavier proteinuria, higher TG and C4d scores, and poorer graft survival.

Conclusions
TG presents clinicopathological features that are distinct from non-TG cases and leads to poorer outcomes. PTC C4d deposition is related to a more rapid progression to graft loss, suggesting ongoing antibody reactivity. HCV-positive TG is a more severe sub-entity, that requires further investigation.
Characterizing sexual histories of women before formal sex-work in south India from a cross-sectional survey: implications for HIV/STI prevention
Authors: Mishra Sharmistha , Ramanaik Satyanarayana , Blanchard James F , Halli Shiva , Moses Stephen , Raghavendra T , Bhattacharjee Parinita , Lorway Rob , Becker Marissa 
Published: September 2012

AbstractBackgroundInterventions designed to prevent HIV and STIs in female sex-workers (FSWs) reach women after they formally enter the sex-trade. We aimed to characterize the pattern of sexual behaviour among FSWs from first-sex to when they identify as sex-workers (transition period) in a region with traditional (historically characterized by dedication into sex-work at first-sex) and non-traditional forms of sex-work.MethodsWe conducted a cross-sectional survey of 246 traditional and 765 non-traditional FSWs across three districts in Karnataka, India. We performed univariate and multivariate logistic regression to profile FSWs most likely to engage in a commercial first-sex before identifying as a sex-worker. Sexual life-course patterns were distinguished using univariate and multivariate linear regression based on key events associated with length of transition period.ResultsOverall, 266 FSWs experienced a commercial first-sex, of whom 45.9% (95% CI: 38.2,53.7) continued a long-term relationship with the first partner. In adjusted analysis, traditional FSWs were more likely to experience a commercial first-sex (AOR 52.5, 95% CI: 27.4,100.7). The average transition time was 8.8 years (SD 3.9), but there was considerable variability between respondents. Among women who experienced a commercial first-sex, a slower transition was independently associated with non-traditional sex-work, the presence of long-term partnerships during the transition period, and ongoing partnerships at time of entry into sex-work. In the absence of a commercial first-sex, a faster transition was associated with traditional sex-work and the dissolution of long-term partnerships, while a slower transition was associated with the presence of long-term partnerships and widowhood. Only 18.5% (95% CI: 12.7,26.2) and 47.3% (95% CI: 32.7,62.3) of women reported ‘always’ condom use with their long-term and occasional partners during the transition period, respectively.ConclusionsFSWs identify as sex-workers several years after becoming sexually active, even when the first-sex is commercial in nature. Long-term partnerships are common after a commercial first-sex, and are associated with a delay in formally entering the sex-trade. The findings call for a better understanding of HIV/STI risk before FSWs identify as sex-workers, and an adaptive programme to reach this period of vulnerability.
Experiences with Surgical treatment of chronic lower limb ulcers at a Tertiary hospital in northwestern Tanzania: A prospective review of 300 cases
Authors: Mbunda Fidelis , Mchembe Mabula D , Chalya Phillipo L , Rambau Peter , Mshana Stephen E , Kidenya Benson R , Gilyoma Japhet M 
Published: September 2012

AbstractBackgroundChronic lower limb ulcers constitute a major public health problem of great important all over the world and contribute significantly to high morbidity and long-term disabilities. There is paucity of information regarding chronic lower limb ulcers in our setting; therefore it was necessary to conduct this study to establish the patterns and outcome of chronic lower limb ulcers and to identify predictors of outcome in our local setting.MethodsThis was a descriptive prospective study of patients with chronic lower limb ulcers conducted at Bugando Medical Centre between November 2010 and April 2012. Ethical approval to conduct the study was sought from relevant authorities. Statistical data analysis was done using SPSS version 17.0 and STATA version 11.0.ResultsA total of 300 patients were studied. Their ages ranged from 3 months to 85 years (median 32 years). The male to female ratio was 2:1. The median duration of illness was 44 days. Traumatic ulcer was the most frequent type of ulcer accounting for 60.3% of patients. The median duration of illness was 44 days. The leg was commonly affected in 33.7% of cases and the right side (48.7%) was frequently involved. Out of 300 patients, 212 (70.7%) had positive aerobic bacterial growth within 48 hours of incubation.Pseudomonas aeruginosa(25.5%) was the most frequent gram negative bacteria isolated, whereas gram positive bacteria commonly isolated wasStaphylococcus aureus(13.7%). Twenty (6.7%) patients were HIV positive with a median CD4+ count of 350 cells/μl. Mycological investigation was not performed. Bony involvement was radiologically reported in 83.0% of cases. Histopathological examination performed in 56 patients revealed malignancy in 20 (35.7%) patients, of which malignant melanoma (45.0%) was the most common histopathological type. The vast majority of patients, 270 (90.0%) were treated surgically, and surgical debridement was the most common surgical procedure performed in 24.1% of cases. Limb amputation rate was 8.7%. Postoperative complication rate was 58.3% of which surgical site infection (77.5%) was the most common post-operative complications. The median length of hospital stay was 23 days. Mortality rate was 4.3%. Out of the two hundred and eighty-seven (95.7%) survivors, 253 (91.6%) were treated successfully and discharged well (healed). After discharge, only 35.5% of cases were available for follow up at the end of study period.ConclusionChronic lower limb ulcers remain a major public health problem in this part of Tanzania. The majority of patients in our environment present late when the disease is already in advanced stages. Early recognition and aggressive treatment of the acute phase of chronic lower limb ulcers at the peripheral hospitals and close follow-up are urgently needed to improve outcomes of these patients in our environment.
Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface
Authors: Chittori Sagar , Savithri Handanahal S , Murthy Mathur RN 
Published: October 2012

Abstract

Background
Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism.

Results
Here we report kinetic characterization of S. typhimurium AckA (St AckA) and structures of its unliganded (Form-I, 2.70 Å resolution) and citrate-bound (Form-II, 1.90 Å resolution) forms. The enzyme showed broad substrate specificity with k

cat
/K

m
in the order of acetate > propionate > formate. Further, the K

m
for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I St AckA represents the first structural report of an unliganded AckA. St AckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (Mt AckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II St AckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II St AckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I St AckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes.

Conclusions
The biochemical and structural characterization of St AckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of St AckA led to identification of a putative ligand-binding pocket at the dimeric interface of St AckA with implications for enzymatic function.
Predicting necrosis in residual mass analysis after retroperitoneal lymph node dissection: a retrospective study
Authors: Miranda Eduardo de Paula , Abe Daniel Kanda , Nesrallah Adriano João , dos Reis Sabrina Thalita , Crippa Alexandre , Srougi Miguel , Dall’Oglio Marcos Francisco 
Published: September 2012

Abstract

Background
Recent studies have demonstrated that pathological analysis of retroperitoneal residual masses of patients with testicular germ cell tumors revealed findings of necrotic debris or fibrosis in up to 50% of patients. We aimed at pursuing a clinical and pathological review of patients undergoing post chemotherapy retroperitoneal lymph node dissection (PC-RPLND) in order to identify variables that may help predict necrosis in the retroperitoneum.

Methods
We performed a retrospective analysis of all patients who underwent PC-RPLND at the University Hospital of the University of São Paulo and Cancer Institute of Sao Paulo between January 2005 and September 2011. Clinical and pathological data were obtained and consisted basically of: measures of retroperitoneal masses, histology of the orchiectomy specimen, serum tumor marker and retroperitoneal nodal size before and after chemotherapy.

Results
We gathered a total of 32 patients with a mean age of 29.7; pathological analysis in our series demonstrated that 15 (47%) had necrosis in residual retroperitoneal masses, 15 had teratoma (47%) and 2 (6.4%) had viable germ cell tumors (GCT). The mean size of the retroperitoneal mass was 4.94 cm in our sample, without a difference between the groups (P = 0.176). From all studied variables, relative changes in retroperitoneal lymph node size (P = 0.04), the absence of teratoma in the orchiectomy specimen (P = 0.03) and the presence of choriocarcinoma in the testicular analysis after orchiectomy (P = 0.03) were statistically significant predictors of the presence of necrosis. A reduction level of 35% was therefore suggested to be the best cutoff for predicting the absence of tumor in the retroperitoneum with a sensitivity of 73.3% and specificity of 82.4%.

Conclusions
Even though retroperitoneal lymph node dissection remains the gold standard for patients with residual masses, those without teratoma in the primary tumor and a shrinkage of 35% or more in retroperitoneal mass have a considerably smaller chance of having viable GCT or teratoma in the retroperitoneum and a surveillance program could be considered.
Study of the oxygen vacancy influence on magnetic properties of Fe- and Co-doped SnO2 diluted alloys
Authors: Borges Pablo D , Scolfaro Luisa M R , Alves Horacio W Leite , da Silva Eronides F , Assali Lucy V C 
Published: September 2012

Abstract
Transition-metal (TM)-doped diluted magnetic oxides (DMOs) have attracted attention from both experimental and theoretical points of view due to their potential use in spintronics towards new nanostructured devices and new technologies. In the present work, we study the magnetic properties of Sn0.96TM0.04O2 and Sn0.96TM0.04O1.98(V
O)0.02, where TM = Fe and Co, focusing in particular in the role played by the presence of O vacancies nearby the TM. The calculated total energy as a function of the total magnetic moment per cell shows a magnetic metastability, corresponding to a ground state, respectively, with 2 and 1 μB/cell, for Fe and Co. Two metastable states, with 0 and 4 μB/cell were found for Fe, and a single value, 3 μB/cell, for Co. The spin-crossover energies (E
S) were calculated. The values are E
S
0/2 = 107 meV and E
S
4/2 = 25 meV for Fe. For Co, E
S
3/1 = 36 meV. By creating O vacancies close to the TM site, we show that the metastablity and E
S change. For iron, a new state appears, and the state with zero magnetic moment disappears. The ground state is 4 μB/cell instead of 2 μB/cell, and the energy E
S
2/4 is 30 meV. For cobalt, the ground state is then found with 3 μB/cell and the metastable state with 1 μB/cell. The spin-crossover energy E
S
1/3 is 21 meV. Our results suggest that these materials may be used in devices for spintronic applications that require different magnetization states.
Antibacterial performance of Ag nanoparticles and AgGO nanocomposites prepared via rapid microwave-assisted synthesis method
Authors: Chook Soon Wei , Chia Chin Hua , Zakaria Sarani , Ayob Mohd Khan , Chee Kah Leong , Huang Nay Ming , Neoh Hui Min , Lim Hong Ngee , Jamal Rahman , Rahman RahaMohdFadhilRajaAbdul 
Published: September 2012

Abstract
Silver nanoparticles and silver-graphene oxide nanocomposites were fabricated using a rapid and green microwave irradiation synthesis method. Silver nanoparticles with narrow size distribution were formed under microwave irradiation for both samples. The silver nanoparticles were distributed randomly on the surface of graphene oxide. The Fourier transform infrared and thermogravimetry analysis results showed that the graphene oxide for the AgNP-graphene oxide (AgGO) sample was partially reduced during the in situ synthesis of silver nanoparticles. Both silver nanoparticles and AgGO nanocomposites exhibited stronger antibacterial properties against Gram-negative bacteria (Salmonella typhi and Escherichia coli) than against Gram-positive bacteria (Staphyloccocus aureus and Staphyloccocus epidermidis). The AgGO nanocomposites consisting of approximately 40 wt.% silver can achieve antibacterial performance comparable to that of neat silver nanoparticles.
Three-dimensional AlZnO/Al2O3/AlZnO nanocapacitor arrays on Si substrate for energy storage
Authors: Li Lian-Jie , Zhu Bao , Ding Shi-Jin , Lu Hong-Liang , Sun Qing-Qing , Jiang Anquan , Zhang David Wei , Zhu Chunxiang 
Published: October 2012

Abstract
High density three-dimensional AZO/Al2O3/AZO nanocapacitor arrays have been fabricated for energy storage applications. Using atomic layer deposition technique, the stack of AZO/Al2O3/AZO has been grown in the porous anodic alumina template which is directly formed on the Si substrate. The fabricated capacitor shows a high capacitance density of 15.3 fF/μm2 at 100 kHz, which is nearly 2.5 times over the planar capacitor under identical conditions in theory. Further, the charge-discharge characteristics of the capacitor are characterized, indicating that the resistance-capacitance time constants are equal to 300 ns for the charging and discharging processes, and have no dependence on the voltage supply. This reflects good power characteristics of the electrostatic capacitor.
Rapid production of antigen-specific monoclonal antibodies from a variety of animals
Authors: Kurosawa Nobuyuki , Yoshioka Megumi , Fujimoto Rika , Yamagishi Fuminori , Isobe Masaharu 
Published: September 2012

AbstractBackgroundAlthough a variety of animals have been used to produce polyclonal antibodies against antigens, the production of antigen-specific monoclonal antibodies from animals remains challenging.ResultsWe propose a simple and rapid strategy to produce monoclonal antibodies from a variety of animals. By staining lymph node cells with an antibody against immunoglobulin and a fluorescent dye specific for the endoplasmic reticulum, plasma/plasmablast cells were identified without using a series of antibodies against lineage markers. By using a fluorescently labeled antigen as a tag for a complementary cell surface immunoglobulin, antigen-specific plasma/plasmablast cells were sorted from the rest of the cell population by fluorescence-activated cell sorting. Amplification of cognate pairs of immunoglobulin heavy and light chain genes followed by DNA transfection into 293FT cells resulted in the highly efficient production of antigen-specific monoclonal antibodies from a variety of immunized animals.ConclusionsOur technology eliminates the need for both cell propagation and screening processes, offering a significant advantage over hybridoma and display strategies.
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network
Authors: Hong Changki , Lee Minho , Kim Dongsup , Kim Dongsan , Cho Kwang-Hyun , Shin Insik 
Published: September 2012

Abstract

Background
Cell cycle process of budding yeast (Saccharomyces cerevisiae) consists of four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to the G1 stationary phase through a sequence of the S, G2 and M phases. During the cell cycle, a cell verifies whether necessary conditions are satisfied at the end of each phase (i.e., checkpoint) since damages of any phase can cause severe cell cycle defect. The cell cycle can proceed to the next phase properly only if checkpoint conditions are met. Over the last decade, there have been several studies to construct Boolean models that capture checkpoint conditions. However, they mostly focused on robustness to network perturbations, and the timing robustness has not been much addressed. Only recently, some studies suggested extension of such models towards timing-robust models, but they have not considered checkpoint conditions.

Results
To construct a timing-robust Boolean model that preserves checkpoint conditions of the budding yeast cell cycle, we used a model verification technique, ‘model checking’. By utilizing automatic and exhaustive verification of model checking, we found that previous models cannot properly capture essential checkpoint conditions in the presence of timing variations. In particular, such models violate the M phase checkpoint condition so that it allows a division of a budding yeast cell into two before the completion of its full DNA replication and synthesis. In this paper, we present a timing-robust model that preserves all the essential checkpoint conditions properly against timing variations. Our simulation results show that the proposed timing-robust model is more robust even against network perturbations and can better represent the nature of cell cycle than previous models.

Conclusions
To our knowledge this is the first work that rigorously examined the timing robustness of the cell cycle process of budding yeast with respect to checkpoint conditions using Boolean models. The proposed timing-robust model is the complete state-of-the-art model that guarantees no violation in terms of checkpoints known to date.
Electronic health records: what does your signature signify?
Authors: Victoroff MD Michael S 
Published: September 2012

Abstract
Electronic health records serve multiple purposes, including clinical communication, legal documentation, financial transaction capture, research and analytics. Electronic signatures attached to entries in EHRs have different logical and legal meanings for different users. Some of these are vestiges from historic paper formats that require reconsideration. Traditionally accepted functions of signatures, such as identity verification, attestation, consent, authorization and non-repudiation can become ambiguous in the context of computer-assisted workflow processes that incorporate functions like logins, auto-fill and audit trails. This article exposes the incompatibility of expectations among typical users of electronically signed information.
Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder
Authors: Steinberg Karyn Meltz , Ramachandran Dhanya , Patel Viren C , Shetty Amol C , Cutler David J , Zwick Michael E 
Published: September 2012

AbstractBackgroundAutism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype.MethodsWe surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility.ResultsWe found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3’ UTR variants did not show statistically significant effects on the expression ofNLGN3andNLGN4X.In addition, we identified twoNLGN3intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation.ConclusionsThese data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects.