A Multiplexed Single-Cell Proteomic Workflow Applicable to Drug Treatment Studies.

It is now well accepted that individual cells within a population will respond to treatment of the same drug in a heterogenous manner. Recent advances have allowed, for the first time, the quantitative analysis of the proteomes of single human cells by mass spectrometry. A major focus of many groups, including our own, has been to use this emerging technology to rapidly identify subpopulations of cells with unique drug response and adaptation methods. While the technology in single-cell proteomics today is progressing at a truly staggering rate, we will detail our current methods for applying highly multiplexed single-cell proteomics to drug treatment studies.

Prevalence of prominent and predominant negative symptoms across different criteria for negative symptom severity and minimal positive symptoms: A comparison of different criteria.

Negative symptoms are a source of disability in schizophrenia, but criteria for identifying patients for clinical trials are in flux. Minimum severity for negative symptoms is paired with a definition of minimal psychosis to identify predominant negative symptoms. Two previous successful negative symptoms treatment studies used very different severity and selection criteria. We compared the prevalence of participants meeting those two criteria in a large outpatient sample of participants with schizophrenia. Data from 867 outpatients with schizophrenia who participated in one of four NIMH-funded studies were analyzed. Common data elements included diagnoses, the PANSS, and an assessment of everyday functioning. We compared previous criterion for premoninant negative symptoms based on low levels of agitation and psychosis and different cut-offs for negative symptoms severity. 57 % of the participants met the agitation-based criteria for low scores and 33 % met the psychosis-based criteria. 18 % met total PANSS score ≥ 20 and 8 % met ≥24 prominent negative symptoms criteria. 14 % met low agitation and PANSS≥20 and 2 % met the low psychosis and negative symptoms ≥24 criteria. Participants who met all predominant criteria had more impairments in social functioning (all p < .001, all d > 0.37). Criteria for predominant negative symptoms from previous clinical trials identify widely different numbers of cases, with criteria for negative symptom severity and low symptoms both impacting. All criteria yield the expected profile of relatively specific social deficits. Even in unselected populations who participated in complex research protocols, 14 % meet low- agitation based criteria for predominant negative symptoms and many more participants would be expected to meet criteria with enrichment for the presence of negative symptoms.

[Benefit assessment of diagnostics - Dealing with incomplete evidence]. / Nutzenbewertung von Diagnostik ­ Umgang mit unvollständiger Evidenz.

Incomplete evidence in diagnostic studies results from missing or too few randomised test-treatment studies or from studies of too low quality. In order to be able to carry out a benefit assessment, it is helpful in the first step to design a hypothetical randomised test-treatment study. In the second step, the linked evidence approach can be used to link the evidence of the individual components of the test-treatment pathway and to assess the potential benefits and risks. In the third step, based on the linked evidence approach, decision analytic models can be used to quantify the benefit-risk ratio. In the case of incomplete evidence, the assessment can thus be made by linking the individual components of the test-treatment pathway, provided that their evidence is sufficient.

The impact of metabolic control on cognition, neurophysiology, and well-being in PKU: A systematic review and meta-analysis of the within-participant literature.

Phenylketonuria (PKU) is a metabolic disease where Phenylalanine (Phe) rises much above normal levels. Cross-sectional and correlational studies provide valuable information on the importance of maintaining low blood-Phe to achieve good outcomes, but they may be confounded, at least partially, by differences in participant demographics. Moreover, the effect of Phe at older ages is difficult to ascertain because of strong associations between Phe levels across ages. Within-participant studies avoid confounding issues. We have reviewed these studies. We followed PRISMA guidelines to search the literature for studies reporting the impact of Phe changes within participants. Phe was either increased or decreased through diet relaxation/resumption or through pharmacological interventions. Forty-six separate articles reported, singly or in combination, results on cognition (N = 37), well-being (N = 22) and neurophysiological health (N = 14). For all studies, we established, in a binary way, whether a benefit of lower Phe was or was not demonstrated and compared numbers showing benefit versus a null or negative outcome. We then analyzed whether critical parameters (e.g., length of the study/condition for the change, size of Phe change achieved) influenced presence or absence of benefit. For a subset of studies that reported quantitative cognitive outcomes, we carried out a meta-analysis to estimate the size of change in cognitive performance associated with a change in Phe and its significance. There were significantly more studies with benefits than no benefits, both for cognitive and well-being outcomes, and a trend in this direction for neurophysiological outcomes. The meta-analysis showed a highly significant effect size both overall (0.55) and when studies with adults/adolescents were considered separately (0.57). There was some indication that benefits were easier to demonstrate when differences in Phe were larger and achieved across a longer period, but these effects were not always consistent. These results reinforce results from the literature by demonstrating the importance of lower Phe in children as well as in adolescents and adults, even when confounding factors in group composition are eliminated. The field would benefit from further studies where Phe levels are contrasted within-participants to ascertain how much Phe needs to be changed and for how long to see a difference and which measures demonstrate a difference (e.g., which cognitive tasks).

A cancer model with nonlocal free boundary dynamics.

Cancer cells at the tumor boundary move in the direction of the oxygen gradient, while cancer cells far within the tumor are in a necrotic state. This paper introduces a simple mathematical model that accounts for these facts. The model consists of cancer cells, cytotoxic T cells, and oxygen satisfying a system of partial differential equations. Some of the model parameters represent the effect of anti-cancer drugs. The tumor boundary is a free boundary whose dynamics is determined by the movement of cancer cells at the boundary. The model is simulated for radially symmetric and axially symmetric tumors, and it is shown that the tumor may increase or decrease in size, depending on the "strength" of the drugs. Existence theorems are proved, global in-time in the radially symmetric case, and local in-time for any shape of tumor. In the radially symmetric case, it is proved, under different conditions, that the tumor may shrink monotonically, or expand monotonically.

Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies.

BACKGROUND: Lung cancer is the number one cancer killer in the world with more than 142,670 deaths estimated in the United States alone in the year 2019. Consequently, there is an overreaching need to identify the key biomarkers for lung cancer. The aim of this study is to computationally identify biomarker genes for lung cancer that can aid in its diagnosis and treatment. The gene expression profiles of two different types of studies, namely non-treatment and treatment, are considered for discovering biomarker genes. In non-treatment studies healthy samples are control and cancer samples are cases. Whereas, in treatment studies, controls are cancer cell lines without treatment and cases are cancer cell lines with treatment. RESULTS: The Differentially Expressed Genes (DEGs) for lung cancer were isolated from Gene Expression Omnibus (GEO) database using R software tool GEO2R. A total of 407 DEGs (254 upregulated and 153 downregulated) from non-treatment studies and 547 DEGs (133 upregulated and 414 downregulated) from treatment studies were isolated. Two Cytoscape apps, namely, CytoHubba and MCODE, were used for identifying biomarker genes from functional networks developed using DEG genes. This study discovered two distinct sets of biomarker genes - one from non-treatment studies and the other from treatment studies, each set containing 16 genes. Survival analysis results show that most non-treatment biomarker genes have prognostic capability by indicating low-expression groups have higher chance of survival compare to high-expression groups. Whereas, most treatment biomarkers have prognostic capability by indicating high-expression groups have higher chance of survival compare to low-expression groups. CONCLUSION: A computational framework is developed to identify biomarker genes for lung cancer using gene expression profiles. Two different types of studies - non-treatment and treatment - are considered for experiment. Most of the biomarker genes from non-treatment studies are part of mitosis and play vital role in DNA repair and cell-cycle regulation. Whereas, most of the biomarker genes from treatment studies are associated to ubiquitination and cellular response to stress. This study discovered a list of biomarkers, which would help experimental scientists to design a lab experiment for further exploration of detail dynamics of lung cancer development.

Survival analysis in rectal carcinoma after neoadjuvant chemoradiation: various methods with different results.

PURPOSE: Survival is an important indicator of outcome quality in rectal carcinoma. The 5-year survival rate is the typical outcome measurement. In patients with neoadjuvant chemoradiation followed by curative surgery, 7 years of follow-up is recommended. Different methods of survival analysis lead to different results. Here, we compared four different methods. METHODS: The data of 439 patients with rectal carcinoma treated with neoadjuvant chemoradiation followed by curative total mesorectal excision (TME) surgery between 1995 and 2010 were analysed. After stratifying by stage, relative survival (RS), cancer-related survival (CRS), overall survival (OS) and disease-free survival (DFS) were compared. In particular, the 3-year disease-free survival rate was compared to the 5- and 7-year overall survival rates. RESULTS: In the total cohort, the 5-year survival rates ranged from 90% (RS), over 84% (CRS) and 83% (OS) to 72% (DFS). Depending on the stage of disease, the differences between the 5-year survival rates varied between 10 and 32 percentage points. The differences were lowest in UICC stage y0 and highest in UICC stage yIV. The 3-year DFS-rate was always lower (worse) than the 5-year OS rate and higher (better) than the 7-year OS rate, with the exception of stage yIV. CONCLUSIONS: Comparisons of survival are only meaningful if the same methods are applied. The 3-year rate of DFS was always worse than the rate of 5-year OS. Therefore, the 3-year rate of DFS appears to be a useful surrogate indicator in rectal carcinoma treatment studies.

Rapid eye movement sleep behavior disorder: devising controlled active treatment studies for symptomatic and neuroprotective therapy--a consensus statement from the International Rapid Eye Movement Sleep Behavior Disorder Study Group.

OBJECTIVES: We aimed to provide a consensus statement by the International Rapid Eye Movement Sleep Behavior Disorder Study Group (IRBD-SG) on devising controlled active treatment studies in rapid eye movement sleep behavior disorder (RBD) and devising studies of neuroprotection against Parkinson disease (PD) and related neurodegeneration in RBD. METHODS: The consensus statement was generated during the fourth IRBD-SG symposium in Marburg, Germany in 2011. The IRBD-SG identified essential methodologic components for a randomized trial in RBD, including potential screening and diagnostic criteria, inclusion and exclusion criteria, primary and secondary outcomes for symptomatic therapy trials (particularly for melatonin and clonazepam), and potential primary and secondary outcomes for eventual trials with disease-modifying and neuroprotective agents. The latter trials are considered urgent, given the high conversion rate from idiopathic RBD (iRBD) to Parkinsonian disorders (i.e., PD, dementia with Lewy bodies [DLB], multiple system atrophy [MSA]). RESULTS: Six inclusion criteria were identified for symptomatic therapy and neuroprotective trials: (1) diagnosis of RBD needs to satisfy the International Classification of Sleep Disorders, second edition, (ICSD-2) criteria; (2) minimum frequency of RBD episodes should preferably be ⩾2 times weekly to allow for assessment of change; (3) if the PD-RBD target population is included, it should be in the early stages of PD defined as Hoehn and Yahr stages 1-3 in Off (untreated); (4) iRBD patients with soft neurologic dysfunction and with operational criteria established by the consensus of study investigators; (5) patients with mild cognitive impairment (MCI); and (6) optimally treated comorbid OSA. Twenty-four exclusion criteria were identified. The primary outcome measure for RBD treatment trials was determined to be the Clinical Global Impression (CGI) efficacy index, consisting of a four-point scale with a four-point side-effect scale. Assessment of video-polysomnographic (vPSG) changes holds promise but is costly and needs further elaboration. Secondary outcome measures include sleep diaries; sleepiness scales; PD sleep scale 2 (PDSS-2); serial motor examinations; cognitive indices; mood and anxiety indices; assessment of frequency of falls, gait impairment, and apathy; fatigue severity scale; and actigraphy and customized bed alarm systems. Consensus also was established for evaluating the clinical and vPSG aspects of RBD. End points for neuroprotective trials in RBD, taking lessons from research in PD, should be focused on the ultimate goal of determining the performance of disease-modifying agents. To date no compound with convincing evidence of disease-modifying or neuroprotective efficacy has been identified in PD. Nevertheless, iRBD patients are considered ideal candidates for neuroprotective studies. CONCLUSIONS: The IRBD-SG provides an important platform for developing multinational collaborative studies on RBD such as on environmental risk factors for iRBD, as recently reported in a peer-reviewed journal article, and on controlled active treatment studies for symptomatic and neuroprotective therapy that emerged during the 2011 consensus conference in Marburg, Germany, as described in our report.

A memory clinic in a department of old-age psychiatry: Its role in clinical and academic research.

Memory clinics are specialist outpatient services offering assessment and evaluation in clinical practice. Memory clinics have been criticized for being preoccupied with research. We analysed the outcomes of 405 referrals to a memory clinic, providing a framework for discussion of the contributions of research to clinical practice. Of the 80% of referrals receiving a formal diagnosis, one-third were recruited on to treatment studies, contributing to clinical research. The remaining two-thirds of patients referred were followed up by specialized care services, and findings from assessment procedures were used to contribute towards academic research. These findings are discussed with reference to the role of research for a memory clinic in clinical practice. The benefits of clinical research are noted, in relation to the percentage of patients involved. The nature of academic research is clarified; it is a dual process, with findings both aiding clinical research and contributing to the body of knowledge about dementia as a possible disease process. It is concluded that memory clinics, as specialized outpatient services, are concerned with research as well as clinical practice, and it is essentially this research which enables clinical practice to develop.