The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

Urinary and sexual function after radical prostatectomy for clinically localized prostate cancer: the Prostate Cancer Outcomes Study

CONTEXT

Patients with prostate cancer and their physicians need knowledge of treatment options and their potential complications, but limited data on complications are available in unselected population-based cohorts of patients.

OBJECTIVE

To measure changes in urinary and sexual function in men who have undergone radical prostatectomy for clinically localized prostate cancer.

DESIGN

The Prostate Cancer Outcomes Study, a population-based longitudinal cohort study with up to 24 months of follow-up.

SETTING

Population-based cancer registries in 6 geographic regions of the United States.

PARTICIPANTS

A total of 1291 black, white, and Hispanic men aged 39 to 79 years who were diagnosed as having primary prostate cancer between October 1, 1994, and October 31, 1995, and who underwent radical prostatectomy within 6 months of diagnosis for clinically localized disease.

MAIN OUTCOME MEASURES

Distribution of and change in urinary and sexual function measures reported by patients at baseline and 6, 12, and 24 months after diagnosis.

RESULTS

At 18 or more months following radical prostatectomy, 8.4% of men were incontinent and 59.9% were impotent. Among men who were potent before surgery, the proportion of men reporting impotence at 18 or more months after surgery varied according to whether the procedure was nerve sparing (65.6% of non-nerve-sparing, 58.6% of unilateral, and 56.0% of bilateral nerve-sparing). At 18 or more months after surgery, 41.9% reported that their sexual performance was a moderate-to-large problem. Both sexual and urinary function varied by age (39.0% of men aged <60 years vs 15.3 %-21.7% of older men were potent at > or =18 months [P<.001]; 13.8% of men aged 75-79 years vs 0.7%-3.6% of younger men experienced the highest level of incontinence at > or =18 months [P = .03]), and sexual function also varied by race (38.4% of black men reported firm erections at > or =18 months vs 25.9% of Hispanic and 21.3% of white men; P = .001).

CONCLUSIONS

Our study suggests that radical prostatectomy is associated with significant erectile dysfunction and some decline in urinary function. These results may be particularly helpful to community-based physicians and their patients with prostate cancer who face difficult treatment decisions.

The P53 pathway: what questions remain to be explored?

The p53 pathway is composed of hundreds of genes and their products that respond to a wide variety of stress signals. These responses to stress include apoptosis, cellular senescence or cell cycle arrest. In addition the p53-regulated genes produce proteins that communicate these stress signals to adjacent cells, prevent and repair damaged DNA and create feedback loops that enhance or attenuate p53 activity and communicate with other signal transduction pathways. Many questions remain to be explored in our understanding of how this network of genes plays a role in protection from cancers, therapy and integrating the homeostatic mechanisms of stress management and fidelity in a cell and organism. The goal of this chapter is to elucidate some of those questions and suggest new directions for this area of research.

The Protein Data Bank and the challenge of structural genomics

The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.

The revolving door of rehospitalization from skilled nursing facilities

Almost one-fourth of Medicare beneficiaries discharged from the hospital to a skilled nursing facility were readmitted to the hospital within thirty days; this cost Medicare $4.34 billion in 2006. Especially in an elderly population, cycling into and out of hospitals can be emotionally upsetting and can increase the likelihood of medical errors related to care coordination. Payment incentives in Medicare do not encourage providers to coordinate beneficiaries' care. Revising these incentives could achieve major savings for providers and improved quality of life for beneficiaries.

The path to healthy ageing in China: a Peking University-Lancet Commission

Around the world, populations are ageing at a faster pace than in the past and this demographic transition will have impacts on all aspects of societies. In May 2020, the UN General Assembly declared 2021–2030 the Decade of Healthy Ageing, highlighting the importance for policymakers across the world to focus policy on improving the lives of older people, both today and in the future. While rapid population ageing poses challenges, China’s rapid economic growth over the last forty years has created space for policy to assist older persons and families in their efforts to improve health and well-being at older ages. As China is home to 1/5 of the world’s older people, China is often held up as an example for other middle-income countries. This Commission Report aims to help readers to understand the process of healthy ageing in China as a means of drawing lessons from the China experience. In addition, with the purpose of informing the ongoing policy dialogue within China, the Commission Report highlights the policy challenges on the horizon and draws lessons from international experience.

Overfeeding rapidly induces leptin and insulin resistance

In common forms of obesity, hyperphagia, hyperinsulinemia, and hyperleptinemia coexist. Here, we demonstrate rapid induction of insulin and leptin resistance by short-term overfeeding. After 3 and 7 days on the assigned diet regimen, rats were tested for their biological responses to acute elevations in plasma insulin and leptin concentrations. Severe resistance to the metabolic effects of both leptin and insulin ensued after just 3 days of overfeeding. During the insulin clamp studies, glucose production was decreased by approximately 70% in control rats and 28-53% in overfed rats. Similarly, leptin infusion doubled the contribution of gluconeogenesis to glucose output in control rats but failed to modify gluconeogenesis in overfed animals. These findings demonstrate a paradoxical and rapid collapse of the leptin system in response to nutrient excess. This partial failure is tightly coupled with the onset of insulin resistance.

Competitive exclusion in a vector-host model for the dengue fever

We study a system of differential equations that models the population dynamics of an SIR vector transmitted disease with two pathogen strains. This model arose from our study of the population dynamics of dengue fever. The dengue virus presents four serotypes each induces host immunity but only certain degree of cross-immunity to heterologous serotypes. Our model has been constructed to study both the epidemiological trends of the disease and conditions that permit coexistence in competing strains. Dengue is in the Americas an epidemic disease and our model reproduces this kind of dynamics. We consider two viral strains and temporary cross-immunity. Our analysis shows the existence of an unstable endemic state ('saddle' point) that produces a long transient behavior where both dengue serotypes cocirculate. Conditions for asymptotic stability of equilibria are discussed supported by numerical simulations. We argue that the existence of competitive exclusion in this system is product of the interplay between the host superinfection process and frequency-dependent (vector to host) contact rates.

Schistosomiasis in the People's Republic of China: prospects and challenges for the 21st century

Schistosomiasis japonica is a serious communicable disease and a major disease risk for more than 30 million people living in the tropical and subtropical zones of China. Infection remains a major public health concern despite 45 years of intensive control efforts. It is estimated that 865,000 people and 100,250 bovines are today infected in the provinces where the disease is endemic, and its transmission continues. Unlike the other schistosome species known to infect humans, the oriental schistosome, Schistosoma japonicum, is a true zoonotic organism, with a range of mammalian reservoirs, making control efforts extremely difficult. Clinical features of schistosomiasis range from fever, headache, and lethargy to severe fibro-obstructive pathology leading to portal hypertension, ascites, and hepatosplenomegaly, which can cause premature death. Infected children are stunted and have cognitive defects impairing memory and learning ability. Current control programs are heavily based on community chemotherapy with a single dose of the drug praziquantel, but vaccines (for use in bovines and humans) in combination with other control strategies are needed to make elimination of the disease possible. In this article, we provide an overview of the biology, epidemiology, clinical features, and prospects for control of oriental schistosomiasis in the People's Republic of China.

Associations of race/ethnicity, education, and dietary intervention with the validity and reliability of a food frequency questionnaire: the Women's Health Trial Feasibility Study in Minority Populations

This report describes the associations of race/ethnicity and years of education with the validity, reliability, and bias of a self-administered food frequency questionnaire (FFQ) designed to be sensitive to low-fat, regional, and ethnic dietary patterns. Data were from the Women's Health Trial Feasibility Study in Minority Populations, a randomized clinical trial conducted between 1992 and 1994 to test the feasibility of a low-fat dietary intervention that targeted low-income, black, and Hispanic women. Of 1,015 participants eligible for these analyses, 28.1% were black, 16.2% were Hispanic, and 12.3% had not completed high school. The analyses focused on percentage of energy obtained from fat, and used 4-day food records as the criterion instrument. Validity at baseline, defined as the correlation between FFQs and food records, was lower among blacks than among whites (0.26 vs. 0.49; p < 0.001), did not differ between Hispanics and whites, and was lower among women with fewer years of education (0.19, 0.35, 0.49, and 0.42 for <12, 12, 13-15, and > or =16 years of education, respectively; for trend, p < 0.05). Six months after randomization, validity increased in most race/ethnicity and education subgroups, and differences across groups became small and statistically nonsignificant. Validity increased significantly among participants receiving the dietary intervention, while increases among control women were somewhat smaller. Reliability, defined as the correlation between baseline and 6-month measures among controls, was similar across racial/ethnic and educational groups. Bias at baseline, defined as the mean value from the FFQ minus the mean from the food record, was 4.6 percentage points of energy from fat; it was lowest among blacks (p < 0.01) and did not differ by years of education. These results suggest that special protocols which address participant training may be necessary when using self-administered FFQs in minority or poorly educated populations.

Long-term care system for older adults in China: policy landscape, challenges, and future prospects

In China, the population is rapidly ageing and the capacity of the system that cares for older people is increasingly a concern. In this Review, we provide a profile of the long-term care system and policy landscape in China. The long-term care system is characterised by rapid growth of the residential care sector, slow development of home and community-based services, and increasing involvement of the private sector. The long-term care workforce shortage and weak quality assurance are concerning. Public long-term care financing is minimal and largely limited to supporting welfare recipients and subsidising the construction of residential care beds and operating costs. China is piloting social insurance long-term care financing models and, concurrently, programmes for integrating health care and long-term care services in selected settings across the country; the effectiveness and sustainability of these pilots remain to be seen. Informed by international long-term care experiences, we offer policy recommendations to strengthen the evolving care system for older people in China.

Optimizing endoscopic biopsy detection of early cancers in Barrett's high-grade dysplasia

OBJECTIVE

The of high-grade dysplasia management (HGD) in Barrett's esophagus remains controversial, in part, because of uncertainty about the ability of endoscopic biopsies to consistently detect early, curable cancers.

METHODS

Here we report cancers we have diagnosed in 45 patients with Barrett's HGD using a protocol involving serial endoscopies with four-quadrant biopsies taken at 1-cm intervals. We compare these results to a modeled endoscopic biopsy protocol in which four-quadrant biopsies are taken every 2 cm in the Barrett's segment.

RESULTS

Thirteen cancers were detected at the baseline endoscopy and 32 in surveillance. In 82% of patients, cancer was detected at a single 1-cm level of the esophagus, and in 69% the cancer was detected in a single endoscopic biopsy specimen. A 2-cm protocol missed 50% of cancers that were detected by a 1-cm protocol in Barrett's segments 2 cm or more without visible lesions. The maximum depth of cancer invasion was intramucosal in 96% of patients. Only 39% of patients who had endoscopic biopsy cancer diagnoses had cancer detected in the esophagectomy specimen. Adverse outcomes included the development of regional metastatic disease during surveillance (1 of 32), operative mortality (3 of 36), including two patients who had their primary surgeries at other institutions, and death from metastatic disease after endoscopic ablation performed at another institution (1 of 3).

CONCLUSIONS

A four-quadrant, 1-cm endoscopic biopsy protocol performed at closely timed intervals consistently detects early cancers arising in HGD in Barrett's esophagus and should be used in patients with HGD who do not undergo surgical resection.

China's rapidly aging population creates policy challenges in shaping a viable long-term care system

In China, formal long-term care services for the large aging population have increased to meet escalating demands as demographic shifts and socioeconomic changes have eroded traditional elder care. We analyze China's evolving long-term care landscape and trace major government policies and private-sector initiatives shaping it. Although home and community-based services remain spotty, institutional care is booming with little regulatory oversight. Chinese policy makers face mounting challenges overseeing the rapidly growing residential care sector, given the tension arising from policy inducements to further institutional growth, a weak regulatory framework, and the lack of enforcement capacity. We recommend addressing the following pressing policy issues: building a balanced system of services and avoiding an "institutional bias" that promotes rapid growth of elder care institutions over home or community-based care; strengthening regulatory oversight and quality assurance with information systems; and prioritizing education and training initiatives to grow a professionalized long-term care workforce.

Separate and unequal: racial segregation and disparities in quality across U.S. nursing homes

We describe the racial segregation in U.S. nursing homes and its relationship to racial disparities in the quality of care. Nursing homes remain relatively segregated, roughly mirroring the residential segregation within metropolitan areas. As a result, blacks are much more likely than whites to be located in nursing homes that have serious deficiencies, lower staffing ratios, and greater financial vulnerability. Changing health care providers' behavior will not be sufficient to eliminate disparities in medical treatment in nursing homes. Persistent segregation among homes poses a substantial barrier to progress.

Work site-based cancer prevention: primary results from the Working Well Trial

OBJECTIVES

This paper presents the behavioral results of the Working Well Trial, the largest US work site cancer prevention and control trial to date.

METHODS

The Working Well Trial used a randomized, matched-pair evaluation design, with the work site as the unit of assignment and analysis. The study was conducted in 111 work sites (n = 28,000 workers). The effects of the intervention were evaluated by comparing changes in intervention and control work sites, as measured in cross-sectional surveys at baseline and follow-up. The 2-year intervention targeted both individuals and the work-site environment.

RESULTS

There occurred a net reduction in the percentage of energy obtained from fat consumption of 0.37 percentage points (P = .033), a net increase in fiber densities of 0.13 g/1000 kcal (P = .056), and an average increase in fruit and vegetable intake of 0.18 servings per day (P = .0001). Changes in tobacco use were in the desired direction but were not significant.

CONCLUSIONS

Significant but small differences were observed for nutrition. Positive trends, but no significant results, were observed in trial-wide smoking outcomes. The observed net differences were small owing to the substantial secular changes in target behaviors.

Glucocorticoid and progesterone inhibit involution and programmed cell death in the mouse mammary gland

Milk production during lactation is a consequence of the suckling stimulus and the presence of glucocorticoids, prolactin, and insulin. After weaning the glucocorticoid hormone level drops, secretory mammary epithelial cells die by programmed cell death and the gland is prepared for a new pregnancy. We studied the role of steroid hormones and prolactin on the mammary gland structure, milk protein synthesis, and on programmed cell death. Slow-release plastic pellets containing individual hormones were implanted into a single mammary gland at lactation. At the same time the pups were removed and the consequences of the release of hormones were investigated histologically and biochemically. We found a local inhibition of involution in the vicinity of deoxycorticosterone- and progesterone-release pellets while prolactin-release pellets were ineffective. Dexamethasone, a very stable and potent glucocorticoid hormone analogue, inhibited involution and programmed cell death in all the mammary glands. It led to an accumulation of milk in the glands and was accompanied by an induction of protein kinase A, AP-1 DNA binding activity and elevated c-fos, junB, and junD mRNA levels. Several potential target genes of AP-1 such as stromelysin-1, c-jun, and SGP-2 that are induced during normal involution were strongly inhibited in dexamethasone-treated animals. Our results suggest that the cross-talk between steroid hormone receptors and AP-1 previously described in cells in culture leads to an impairment of AP-1 activity and to an inhibition of involution in the mammary gland implying that programmed cell death in the postlactational mammary gland depends on functional AP-1.

Cell of origin determines clinically relevant subtypes of MLL-rearranged AML

Mixed lineage leukemia (MLL)-fusion proteins can induce acute myeloid leukemias (AMLs) from either hematopoietic stem cells (HSCs) or granulocyte-macrophage progenitors (GMPs), but it remains unclear whether the cell of origin influences the biology of the resultant leukemia. MLL-AF9-transduced single HSCs or GMPs could be continuously replated, but HSC-derived clones were more likely than GMP-derived clones to initiate AML in mice. Leukemia stem cells derived from either HSCs or GMPs had a similar immunophenotype consistent with a maturing myeloid cell (LGMP). Gene expression analyses demonstrated that LGMP inherited gene expression programs from the cell of origin including high-level Evi-1 expression in HSC-derived LGMP. The gene expression signature of LGMP derived from HSCs was enriched in poor prognosis human MLL-rearranged AML in three independent data sets. Moreover, global 5'-mC levels were elevated in HSC-derived leukemias as compared with GMP-derived leukemias. This mirrored a difference seen in 5'-mC between MLL-rearranged human leukemias that are either EVI1 positive or EVI1 negative. Finally, HSC-derived leukemias were more resistant to chemotherapy than GMP-derived leukemias. These data demonstrate that the cell of origin influences the gene expression profile, the epigenetic state and the drug response in AML, and that these differences can account for clinical heterogeneity within a molecularly defined group of leukemias.

Blood compatibility of amorphous titanium oxide films synthesized by ion beam enhanced deposition

Titanium oxide films were synthesized on titanium, cobalt alloy and low-temperature isotropic pryolytic carbon by ion beam enhanced deposition. The non-stoichiometrical titanium oxide films were obtained. Blood compatibility of the films were evaluated by clotting time measurement, platelet adhesion investigation and hemolysis analyses. The results revealed that blood compatibility of the materials was improved by the coating of titanium oxide films. Semiconductor nature of non-stoichiometric titanium oxide films might be responsible for the improvement of blood compatibility.

A model for tuberculosis with exogenous reinfection

Following primary tuberculosis (TB) infection, only approximately 10% of individuals develop active T.B. Most people are assumed to mount an effective immune response to the initial infection that limits proliferation of the bacilli and leads to long-lasting partial immunity both to further infection and to reactivation of latent bacilli remaining from the original infection. Infected individuals may develop active TB as a consequence of exogenous reinfection, i.e., acquiring a new infection from another infectious individual. Our results in this paper suggest that exogenous reinfection has a drastic effect on the qualitative dynamics of TB. The incorporation of exogenous reinfection into our TB model allows the possibility of a subcritical bifurcation at the critical value of the basic reproductive number R(0)=1, and hence the existence of multiple endemic equilibria for R(0)<1 and the exogenous reinfection rate larger than a threshold. Our results suggest that reducing R(0) to be smaller than one may not be sufficient to eradicate the disease. An additional reduction in reinfection rate may be required. These results may also partially explain the recently observed resurgence of TB.

Monitoring free flaps using the laser Doppler flowmeter: five-year experience

Over a 5-year period, 232 microvascular composite-tissue transfers to the head and neck, trunk, and extremities were monitored using the laser Doppler flowmeter. Thirteen free flaps (5.6 percent) developed vascular complications, all within 4 days after surgery. The laser Doppler flowmeter detected vascular compromise in all cases with no false positives or negatives. Failure to monitor the flap according to protocol by nursing staff occurred in one patient, which led to a delay in detection of venous compromise and subsequent flap loss. The salvage rate was 69.2 percent, leading to an overall flap viability of 98.3 percent. Our series of free-flap monitoring using the laser Doppler flowmeter is the largest reported to date. Review of the English literature shows consistent support by numerous clinical series for the use of the laser Doppler as a valuable postoperative monitor after free-flap transfers.

The Care Span: Growth of racial and ethnic minorities in US nursing homes driven by demographics and possible disparities in options

Between 1999 and 2008, the number of elderly Hispanics and Asians living in US nursing homes grew by 54.9 percent and 54.1 percent, respectively, while the number of elderly black residents increased 10.8 percent. During the same period, the number of white nursing home residents declined 10.2 percent. These shifts have been driven in part by changing demographics, especially the fast growth of older minority populations. However, the numbers of minority residents in nursing homes increased more rapidly than the minority population overall, even in areas with high concentrations of minority populations. Thus, these results may indicate unequal minority access to home and community-based alternatives, which are generally preferred for long-term care. When designing initiatives to balance institutional and noninstitutional long-term care, policy makers should take steps to reduce racial and ethnic disparities.

NF-kappa B activation mediates doxorubicin-induced cell death in N-type neuroblastoma cells

Neuroblastoma is the most common extracranial solid tumor of childhood. N-type neuroblastoma cells (represented by SH-SY5Y and IMR32 cell lines) are characterized by a neuronal phenotype. N-type cell lines are generally N-myc amplified, express the anti-apoptotic protein Bcl-2, and do not express caspase-8. The present study was designed to determine the mechanism by which N-type cells die in response to specific cytotoxic agents (such as cisplatin and doxorubicin) commonly used to treat this disease. We found that N-type cells were equally sensitive to cisplatin and doxorubicin. Yet death induced by cisplatin was inhibited by the nonselective caspase inhibitor z-Val-Ala-Asp-fluoromethylketone or the specific caspase-9 inhibitor N-acetyl-Leu-Glu-His-Asp-aldehyde, whereas in contrast, caspase inhibition did not prevent doxorubicin-induced death. Neither the reactive oxygen species nor the mitochondrial permeability transition appears to play an important role in this process. Doxorubicin induced NF-kappa B transcriptional activation in association with I-kappa B alpha degradation prior to loss of cell viability. Surprisingly, the antioxidant and NF-kappa B inhibitor pyrrolidine dithiocarbamate blocked doxorubicin-induced NF-kappa B transcriptional activation and provided profound protection against doxorubicin killing. Moreover, SH-SY5Y cells expressing a super-repressor form of I-kappa B were completely resistant to doxorubicin killing. Together these findings show that NF-kappa B activation mediates doxorubicin-induced cell death without evidence of caspase function and suggest that cisplatin and doxorubicin engage different death pathways to kill neuroblastoma cells.

Use of physical restraints and antipsychotic medications in nursing homes: a cross-national study

OBJECTIVES

This study compares inter- and intra-country differences in the prevalence of physical restraints and antipsychotic medications in nursing homes, and examines aggregated resident conditions and organizational characteristics correlated with these treatments.

METHODS

Population-based, cross-sectional data were collected using a standardized Resident Assessment Instrument (RAI) from 14,504 long-term care facilities providing nursing home level services in five countries participating in the interRAI consortium, including Canada, Finland, Hong Kong (Special Administrative Region, China), Switzerland, and the United States. Facility-level prevalence rates of physical restraints and antipsychotic use were examined both between and within the study countries.

RESULTS

The prevalence of physical restraint use varied more than five-fold across the study countries, from an average 6% in Switzerland, 9% in the US, 20% in Hong Kong, 28% in Finland, and over 31% in Canada. The prevalence of antipsychotic use ranged from 11% in Hong Kong, between 26-27% in Canada and the US, 34% in Switzerland, and nearly 38% in Finland. Within each country, substantial variations existed across facilities in both physical restraint and antipsychotic use rates. In all countries, neither facility case mix nor organizational characteristics were particularly predictive of the prevalence of either treatment.

CONCLUSIONS

There exists large, unexplained variability in the prevalence of physical restraint and antipsychotic use in nursing home facilities both between and within countries. Since restraints and antipsychotics are associated with adverse outcomes, it is important to understand the idiosyncratic factors specific to each country that contribute to variation in use rates.