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An introduction to the software package DELTA (DEscription Language for TAxonomy) is given. Th e contribution consists of step by step instructions into the DELTA Editor and the interactive identification program Intkey. It describes how to record taxonomic character information in a database and maintain these data. Standard output functions are simplified in a new starter database. All used commands are commented and it is marked where changes in the command files are required. Th e paper explains how to generate text descriptions, interactive identification tools, and how to make keys and species diagnoses. [ABSTRACT FROM AUTHOR]

Abstract Background SAMHD1 is an HIV-1 restriction factor in non-dividing monocytes, dendritic cells (DCs), macrophages, and resting CD4+ T-cells. Acting as a deoxynucleoside triphosphate (dNTP) triphosphohydrolase, SAMHD1 hydrolyzes dNTPs and restricts HIV-1 infection in macrophages and resting CD4+ T-cells by decreasing the intracellular dNTP pool. However, the intracellular dNTP pool in DCs and its regulation by SAMHD1 remain unclear. SAMHD1 has been reported as a type I interferon (IFN)-inducible protein, but whether type I IFNs upregulate SAMHD1 expression in primary DCs and CD4+ T-lymphocytes is unknown. Results Here, we report that SAMHD1 significantly blocked single-cycle and replication-competent HIV-1 infection of DCs by decreasing the intracellular dNTP pool and thereby limiting the accumulation of HIV-1 late reverse transcription products. Type I IFN treatment did not upregulate endogenous SAMHD1 expression in primary DCs or CD4+ T-lymphocytes, but did in HEK 293T and HeLa cell lines. When SAMHD1 was over-expressed in these two cell lines to achieve higher levels than that in DCs, no HIV-1 restriction was observed despite partially reducing the intracellular dNTP pool. Conclusions Our results suggest that SAMHD1-mediated reduction of the intracellular dNTP pool in DCs is a common mechanism of HIV-1 restriction in myeloid cells. Endogenous expression of SAMHD1 in primary DCs or CD4+ T-lymphocytes is not upregulated by type I IFNs.

Abstract Background Dendritic cells (DCs) are among the first cells to encounter HIV-1 and play important roles in viral transmission and pathogenesis. Immature DCs allow productive HIV-1 replication and long-term viral dissemination. The pro-inflammatory factor lipopolysaccharide (LPS) induces DC maturation and enhances the efficiency of DC-mediated HIV-1 transmission. Type I interferon (IFN) partially inhibits HIV-1 replication and cell-cell transmission in CD4+ T cells and macrophages. Tetherin is a type I IFN-inducible restriction factor that blocks HIV-1 release and modulates CD4+ T cell-mediated cell-to-cell transmission of HIV-1. However, the role of type I IFN and tetherin in HIV-1 infection of DCs and DC-mediated viral transmission remains unknown. Results We demonstrated that IFN-alpha (IFNα)-induced mature DCs restricted HIV-1 replication and trans-infection of CD4+ T cells. Tetherin expression in monocyte-derived immature DCs was undetectable or very low. High levels of tetherin were transiently expressed in LPS- and IFNα-induced mature DCs, while HIV-1 localized into distinct patches in these DCs. Knockdown of induced tetherin in LPS- or IFNα-matured DCs modestly enhanced HIV-1 transmission to CD4+ T cells, but had no significant effect on wild-type HIV-1 replication in mature DCs. Intriguingly, we found that HIV-1 replication in immature DCs induced significant tetherin expression in a Nef-dependent manner. Conclusions The restriction of HIV-1 replication and transmission in IFNα-induced mature DCs indicates a potent anti-HIV-1 response; however, high levels of tetherin induced in mature DCs cannot significantly restrict wild-type HIV-1 release and DC-mediated HIV-1 transmission. Nef-dependent tetherin induction in HIV-1-infected immature DCs suggests an innate immune response of DCs to HIV-1 infection.

Abstract Background Obesity has reached epidemic proportions in the United States. It is implicated in the development of a variety of chronic disease states and is associated with increased levels of inflammation and oxidative stress. The objective of this study is to examine the effect of Medifast's meal replacement program (MD) on body weight, body composition, and biomarkers of inflammation and oxidative stress among obese individuals following a period of weight loss and weight maintenance compared to a an isocaloric, food-based diet (FB). Methods This 40-week randomized, controlled clinical trial included 90 obese adults with a body mass index (BMI) between 30 and 50 kg/m2, randomly assigned to one of two weight loss programs for 16 weeks and then followed for a 24-week period of weight maintenance. The dietary interventions consisted of Medifast's meal replacement program for weight loss and weight maintenance, or a self-selected, isocaloric, food-based meal plan. Results Weight loss at 16 weeks was significantly better in the Medifast group (MD) versus the food-based group (FB) (12.3% vs. 6.9%), and while significantly more weight was regained during weight maintenance on MD versus FB, overall greater weight loss was achieved on MD versus FB. Significantly more of the MD participants lost ≥ 5% of their initial weight at week 16 (93% vs. 55%) and week 40 (62% vs. 30%). There was no difference in satiety observed between the two groups during the weight loss phase. Significant improvements in body composition were also observed in MD participants compared to FB at week 16 and week 40. At week 40, both groups experienced improvements in biochemical outcomes and other clinical indicators. Conclusions Our data suggest that the meal replacement diet plan evaluated was an effective strategy for producing robust initial weight loss and for achieving improvements in a number of health-related parameters during weight maintenance, including inflammation and oxidative stress, two key factors more recently shown to underlie our most common chronic diseases. Trial Registration ClinicalTrials.gov NCT01011491

Abstract HIV is a devastating human pathogen that causes serious immunological diseases in humans around the world. The virus is able to remain latent in an infected host for many years, allowing for the long-term survival of the virus and inevitably prolonging the infection process. The location and mechanisms of HIV latency are under investigation and remain important topics in the study of viral pathogenesis. Given that HIV is a blood-borne pathogen, a number of cell types have been proposed to be the sites of latency, including resting memory CD4+ T cells, peripheral blood monocytes, dendritic cells and macrophages in the lymph nodes, and haematopoietic stem cells in the bone marrow. This review updates the latest advances in the study of HIV interactions with monocytes and dendritic cells, and highlights the potential role of these cells as viral reservoirs and the effects of the HIV-host-cell interactions on viral pathogenesis.

Background: Countries are increasingly devoting significant resources to creating or strengthening research ethics committees, but there has been insufficient attention to assessing whether these committees are actually improving the protection of human research participants.Discussion: Research ethics committees face numerous obstacles to achieving their goal of improving research participant protection. These include the inherently amorphous nature of ethics review, the tendency of regulatory systems to encourage a focus on form over substance, financial and resource constraints, and conflicts of interest. Auditing and accreditation programs can improve the quality of ethics review by encouraging the development of standardized policies and procedures, promoting a common base of knowledge, and enhancing the status of research ethics committees within their own institutions. However, these mechanisms focus largely on questions of structure and process and are therefore incapable of answering many critical questions about ethics committees' actual impact on research practices. The first step in determining whether research ethics committees are achieving their intended function is to identify what prospective research participants and their communities hope to get out of the ethics review process. Answers to this question can help guide the development of effective outcomes assessment measures. It is also important to determine whether research ethics committees' guidance to investigators is actually being followed. Finally, the information developed through outcomes assessment must be disseminated to key decision-makers and incorporated into practice. This article offers concrete suggestions for achieving these goals.Conclusion: Outcomes assessment of research ethics committees should address the following questions: First, does research ethics committee review improve participants' understanding of the risks and potential benefits of studies? Second, does the process affect prospective participants' decisions about whether to participate in research? Third, does it change participants' subjective experiences in studies or their attitudes about research? Fourth, does it reduce the riskiness of research? Fifth, does it result in more research responsive to the local community's self-identified needs? Sixth, is research ethics committees' guidance to researchers actually being followed? [ABSTRACT FROM AUTHOR]

In response to the increasing number of mentally ill people experiencing homelessness, some policy-makers have called for the expanded use of involuntary commitment, even for individuals who are not engaging in behaviors that are immediately life-threatening. Yet there is no evidence that involuntary commitment offers long-term benefits, and significant reasons to believe that expanding the practice will cause harm. In addition, these proposals ignore research showing that most people with mental illness have the capacity to make medical decisions for themselves. Rather than expanding the use of involuntary commitment, policy-makers should support approaches proven to decrease the prevalence of homelessness, such as supportive housing. In addition, states should reevaluate their commitment standards for persons who pose no risk of harm to others. One promising approach is Northern Ireland's Mental Health Capacity Act of 2016, which establishes a uniform standard for imposing nonconsensual health care interventions, without any distinction between mental illnesses and other conditions in which capacity might be compromised., (© 2024 The Hastings Center.)

Under the Common Rule, federally-supported activities involving human participants are presumptively required to undergo prospective ethics review if they are "designed to develop or contribute to generalizable knowledge." However, the "generalizable knowledge" standard is inherently ambiguous; moreover, it is both over- and under-inclusive of the type of activities that warrant prospective ethical oversight. Rather than conditioning prospective ethics review on an ethically irrelevant criterion like the generalizable knowledge standard, this article proposes that prior ethics review should be required when some individuals are exposed to greater-than-minimal risks for the potential benefit of others, at least when the activity in question is conducted or supported by federal agencies. Under such an approach, the fact that an activity constitutes research would be neither necessary nor sufficient to trigger prospective ethical oversight.

The revised Common Rule contains several changes designed to reduce the time institutional review boards (IRBs) spend on overseeing low-risk studies, including an expansion of the categories of research that are exempt from the regulations and a list of specific activities that do not satisfy the regulatory definition of "research." While these changes go a long way toward the goal of reducing unnecessarily regulatory burden, they leave several important questions about IRB jurisdiction unresolved.  The most significant omission is the failure to address when IRB review is necessary for quality assurance activities.  In addition, the revised Common Rule's distinction between "research" and "public health surveillance" may prove to be unworkable as applied to some types of public health activities.  Many of these interpretive questions stem from the inherent ambiguities in the regulatory definition of research, which turns on whether an activity is "designed to develop or contribute to generalizable knowledge." Because the revised Common Rule does not alter this basic definition, difficult questions about the circumstances in which IRB review is required are likely to remain., (Copyright© 2017 The Hastings Center.)

Developing countries face numerous barriers to conducting effective and efficient ethics reviews of international collaborative research. In addition to potentially overlooking important scientific and ethical considerations, inadequate or insufficiently trained ethics committees may insist on unwarranted changes to protocols that can impair a study's scientific or ethical validity. Moreover, poorly functioning review systems can impose substantial delays on the commencement of research, which needlessly undermine the development of new interventions for urgent medical needs. In response to these concerns, the Drugs for Neglected Diseases Initiative (DNDi), an independent nonprofit organization founded by a coalition of public sector and international organizations, developed a mechanism to facilitate more effective and efficient host country ethics review for a study of the use of fexinidazole for the treatment of late stage African Trypanosomiasis (HAT). The project involved the implementation of a novel 'pre-review' process of ethical oversight, conducted by an ad hoc committee of ethics committee representatives from African and European countries, in collaboration with internationally recognized scientific experts. This article examines the process and outcomes of this collaborative process., (© 2014 The Authors. Developing World Bioethics published by John Wiley & Sons Ltd.)

The increased focus in recent years on the risks posed by conflicts of interest arising from financial relationships between physician-investigators and the pharmaceutical and medical device industries has led to a variety of measures that can broadly be described as "regulatory" interventions, including new federal and state laws, criminal prosecutions and private lawsuits, requirements attached to government funding, and institutional policies. Studies suggest, however, that physician-investigators have not internalized the message that financial conflicts of interest have the potential to influence their decision making. Simply informing physician-investigators of the content of relevant rules and the consequences of noncompliance - as appears to be the practice in many existing compliance training activities - is unlikely to lead to lasting changes in norms or behavior. Instead, we theorize that, for trainings to be maximally effective, they must appeal to the complex intrinsic and extrinsic motivations that contribute to individuals' willingness to comply with regulatory mandates. In addition, physician-investigators' beliefs that the risks posed by conflicts of interest do not apply to them need to be challenged. Rigorous evaluation of the newly-designed training programs will help determine whether these theories are borne out in fact., (© 2012 American Society of Law, Medicine & Ethics, Inc.)

This article examines and critiques the use of the term "vulnerability" in U.S. and international regulations and guidelines on research ethics. After concluding that the term is currently used in multiple, often inconsistent, senses, it calls on regulators to differentiate between three distinct types of vulnerability: "consent-based vulnerability,""risk-based vulnerability," and "justice-based vulnerability."

Applying the Americans with Disabilities Act (ADA) to denials of treatment by assisted reproductive technology (ART) practitioners raises particularly challenging legal and ethical issues. On the one hand, the danger that physicians will inappropriately deny treatment to patients with disabilities is especially worrisome in the context of ARTs, given the widespread stigma associated with reproduction by individuals with disabilities. On the other hand, patients' disabilities may sometimes have potentially devastating implications for any child resulting from treatment, including the possibility that the child will be born with life-threatening or seriously debilitating impairments. Some physicians have strong ethical objections to helping patients become pregnant in the face of such risks. In this Article, Professor Coleman develops a framework for applying the ADA to disability-based denials of ARTs that addresses these competing considerations. In recognizing risks to the future child as a potential defense to a disability discrimination claim, Professor Coleman rejects the view of some commentators that such risks are relevant to reproductive decisions only if the child is likely to suffer so much that he or she would prefer not to exist. Instead, he proposes that, when a patient's disabilities create significant risks to the future child, the question should not be whether the child's life is likely to be so awful that nonexistence would be preferable, but how the risks and benefits of the requested treatment compare to those associated with other available reproductive and parenting options. Professor Coleman provides a theoretical justification for adopting this comparative framework, and examines how ADA precedents developed in other contexts should be applied to decisions about ARTs.

The New York State Task Force on Life and the Law, a state bioethical policy commission, recently completed a project addressing the ethical, legal, and social concerns surrounding the predictive uses of genetic testing. Its report, Genetic Testing and Screening in the Age of Genomic Medicine, makes legislative, public policy, and practice recommendations on a host of issues. As part of this project, the Task Force reviewed the current policy and legislative landscapes related to confidentiality protections for genetic information and the use of genetic information by insurers. It also assessed requirements for informed consent to clinical genetic testing and for the use of clinical samples for genetics research. The Task Force considered gaps and unintended consequences of relevant genetic testing legislation and assessed its flexibility to address new uses of genetic testing, such as pharmacogenetic testing, and new ways of offering tests, such as multiplex testing panels. The Task Force also considered the relevance of the pleiotropic characteristic of genes for issues of informed consent to genetic testing and the confidentiality of genetic information. The Task Force's recommendations, presented here, seek to promote the appropriate uses of clinical genetic testing and research while preventing potential harms.