bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models
Authors: Khandelwal Garima , Girotti María Romina , Smowton Christopher , Taylor Sam , Wirth Christopher , Dynowski Marek , Frese Kristopher K. , Brady Ged , Dive Caroline , Marais Richard , Miller Crispin 
Published: April 2017

Abstract
Patient-derived xenograft (PDX) and circulating tumor cell–derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions, including the study of metastatic progression, genetic evolution, and therapeutic drug responses. As PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis. When used for this purpose, their reliability is highly dependent on being able to accurately distinguish between sequencing reads that originate from the host, and those that arise from the xenograft itself. Here, we demonstrate that failure to correctly identify contaminating host reads when analyzing DNA- and RNA-sequencing (DNA-Seq and RNA-Seq) data from PDX and CDX models is a major confounding factor that can lead to incorrect mutation calls and a failure to identify canonical mutation signatures associated with tumorigenicity. In addition, a highly sensitive algorithm and open source software tool for identifying and removing contaminating host sequences is described. Importantly, when applied to PDX and CDX models of melanoma, these data demonstrate its utility as a sensitive and selective tool for the correction of PDX- and CDX-derived whole-exome and RNA-Seq data.
Implications: This study describes a sensitive method to identify contaminating host reads in xenograft and explant DNA- and RNA-Seq data and is applicable to other forms of deep sequencing. Mol Cancer Res; 15(8); 1012–6. ©2017 AACR.
Therapeutic Targeting of PTK7 is Cytotoxic in Atypical Teratoid Rhabdoid Tumors
Authors: Messerli Shanta M. , Hoffman Mariah M. , Gnimpieba Etienne Z. , Bhardwaj Ratan D. 
Published: April 2017

Abstract
Novel discoveries involving the evaluation of potential therapeutics are based on newly identified molecular targets for atypical teratoid rhabdoid tumors (ATRT), which are the most common form of infantile brain tumors. Central nervous system ATRTs are rare, aggressive, and fast growing tumors of the brain and spinal cord and carry a very poor prognosis. Currently, the standard of care for ATRT patients is based on surgical resection followed by systemic chemotherapy and radiotherapy, which result in severe side effects. As protein tyrosine kinases have proven to be actionable targets that reduce tumor growth in a number of cancers, we examined how inhibiting tyrosine kinases affected ATRT tumor growth. Here, we examine the therapeutic efficacy of the broad-spectrum tyrosine kinase inhibitor vatalanib in the treatment of ATRT. Vatalanib significantly reduced the growth of ATRT tumor cell lines, both in two-dimensional cell culture and in three-dimensional cell culture using a spheroid model. As vatalanib had a remarkable effect on the growth of ATRT, we decided to use a transcriptomic approach to therapy by examining new actionable targets, such as tyrosine kinases. Next-generation RNA-sequencing and NanoString data analysis showed a significant increase in PTK7 RNA expression levels in ATRT tumors. Inhibition of PTK7 by siRNA treatment significantly decreases the viability of ATRT patient–derived tumor cell lines.
Implications: These studies provide the groundwork for future preclinical in vivo studies aiming to investigate the efficacy of PTK7 inhibition on ATRT tumor growth. Mol Cancer Res; 15(8); 973–83. ©2017 AACR.
<b>Host specificity of some wood decaying-fungi in moist deciduous forests of Kerala, India</b>
Authors: Iqbal A. Muhammed , Vidyasagaran Kattany , Ganesh Narayan 
Published: April 2017

The low diversity tropical forest is dominated by host specialized wood decaying fungi (Hymenochaetales, Polyporales) with narrow host range. To understand whether or not wood decaying fungi in a highly diverse tropical moist deciduous forest have any kind of host specialization, sporophores of 22 species of wood decaying fungi were recorded on 17 tree species in three seasons viz., pre monsoon, monsoon and post monsoon from the moist deciduous forests of Peechi-Vazhani Wildlife Sanctuary, Kerala, India. Only two of the 22 species with three or more records showed signs of host specialization. In the case of other fungi, the number of host tree species increased with increasing number of occupied or colonized logs. The findings support the assumption that most of the wood decaying fungi have broad host ranges in highly diverse forest types in the tropics.
<b>Conservation of the Southern River Terrapin <I>Batagur affinis</I> (Reptilia: Testudines: Geoemydidae) in Malaysia: a case study involving local community participation</b>
Authors: Chen Pelf Nyok 
Published: April 2017

It is evident that the participation of the local community plays a crucial role in the success of a conservation project. Despite initiating and leading the oldest Batagur affinis conservation project in Malaysia since 1967, which involved egg protection, head starting and reintroduction programs, the Department of Wildlife and National Parks did not involve the participation of the local community. This study provides the first account of the involvement of local villagers in B. affinis research and conservation project in the Kemaman River, Terengganu, Malaysia. As a result of involving this group of local villagers, the Village Development and Security Committee was recruited to be involved in the conservation project. From 2012 to 2016, we hand captured and processed 102 post-nesting females. The Schnabel mark-recapture method estimated at least 186 wild female B. affinis in the river. We collected 2,542 B. affinis eggs from 205 nests for incubation, and produced 1,723 hatchlings (mean hatching success 67.8%). Survivorship of head started B. affinis hatchlings in captivity ranged from 96.7−100 % among cohorts. Head started hatchlings recorded a 467% increase in body mass and 90% increase in straight carapace length. We reintroduced 1,690 B. affinis juveniles into the river. We also initiated a symbolic adoption program to raise funds and ensure the sustainability of the conservation project. This study proves that local communities are capable of managing their own resources, given sufficient training in conservation techniques.
A Simple New Model for Incoming Solar Radiation Dependent Only on Screen-Level Relative Humidity
Authors: Lindauer M. , Schmid H. P. , Grote R. , Steinbrecher R. , Mauder M. , Wolpert B. 
Published: April 2017

AbstractGlobal incoming shortwave radiation (Rg) is the energy source for the majority of biogeochemical processes on Earth as well as for photovoltaic power production. Existing simple site-specific models to estimate Rg commonly use the daily range of air temperature as input variables. Here, the authors present a simple model for incoming shortwave radiation, requiring only screen-level relative humidity data (and site-specific astronomical information). The model was developed and parameterized using high-quality global radiation data covering a broad range of climate conditions. It was evaluated at independent sites, which were not involved in the process of model development and parameterization. The mean 1:1 slope was 1.02 with an averager2of 0.98. Normalized root-mean-square error (NRMSE) averaged at 43%. Despite its simplicity, the new model clearly outperforms conventional approaches, and it comes close to more labor- and data-intensive alternative models.
The Coproduction of Truancy Control
Authors: Mazerolle Lorraine , Bennett Sarah , Antrobus Emma , Eggins Elizabeth 
Published: April 2017

Objectives: To evaluate, under randomized field trial conditions, the deterrent effects of a police–school partnership, called the Ability School Engagement Program (ASEP). The partnership sought to co-produce truancy reduction by actively engaging parents and their truanting children in a group conference dialogue that was designed to increase parental and child awareness of the truancy laws (and the consequences of noncompliance), and thereby foster students’ willingness to attend school. Methods: Using a randomized field trial design, 102 truanting young people were randomly allocated to a control, business-as-usual condition ( n = 51), or the ASEP experimental condition ( n = 51). In this paper, we use mixed model ANOVA and multiple regression analysis of self-report survey data from both students and their parents to assess differences between the experimental and control group on parental perceptions of prosecution likelihood and student willingness to attend school. We use qualitative analysis of the group conference transcripts to examine how the intervention affected these factors. Results: Our results demonstrate that the police–school partnership intervention increased parental awareness of prosecution likelihood, which moderated students’ self-reported willingness to attend school. Conclusions: We conclude that police–school partnerships that engage parents and their children to better understand the laws pertaining to school attendance are a promising approach for co-producing the reduction of truancy.
Comfort signatures: How long-term studies of occupant satisfaction in office buildings reveal on-going performance
Authors: Bunn Roderic , Marjanovic-Halburd Ljiljana 
Published: April 2017

Occupant surveys reveal how people in buildings perceive their internal environments. The Soft Landings extended handover process, which requires project teams to focus more on operational outcomes, has led to the use of occupant surveys during a three year Soft Landings aftercare period to provide a means of checking whether the desired outcomes have been met. However, little is known of the longitudinal perceptions of occupant satisfaction in buildings, and the relationships between those perceptions and the many environmental, seasonal and functional comfort variables that act upon occupant satisfaction. This paper reports the results of time-series surveys on two office buildings. Occupant satisfaction scores have been compared with the technical, organisational and functional contexts in the work environments, such as density, workgroup sizes, and cellular and open-plan layouts, to determine whether changes in these parameters have significantly altered levels of perceived occupant comfort and productivity. The research found stability in some contexts but statistical declines in others. Conclusions are made regarding the key operational factors that may contribute to changes in occupant satisfaction over time. Factors that might constitute limits to office carrying capacity are discussed. Practical application: The growing use of the Soft Landings approach to building procurement and handover, with greater emphasis on designing for improved operational outcomes, is creating a demand to understand more about occupant needs and expectations. The central government equivalent – Government Soft Landings – is similarly placing a requirement on public sector construction projects to deliver buildings with improved environmental and functional outcomes. Delivering these expectations requires construction professionals to develop skills in building performance evaluation, particularly in understanding the primary drivers that lead to high occupant perceptions of comfort, health, productivity and wellbeing. This research provides real-world evidence to clients and their design advisors on the key factors for ensuring long-term occupant satisfaction, while for building management professionals the research identifies some organisational risk factors that may lead to a fall in satisfaction during long-term operation.
Patient emergency assessment following deliberate self-poisoning with benzodiazepines: Can cognitive markers predict recall of the psychiatric interview? A pilot study
Authors: Salles J , Pariente J , Dimeglio C , Gandia P , Lemesle B , Giron A , Franchitto N , Schmitt L , Very E 
Published: April 2017

Study hypothesis: In cases of deliberate self-poisoning (DSP), patients often ingest benzodiazepines (BZDs), known to alter memory. Experts recommend recovery of the patient’s cognitive capacity before psychiatric assessment. Unfortunately, there is no validated tool in common practice to assess whether sufficient cognitive recovery has occurred after DSP with BZDs to ensure patient memory of the assessment. Objective: The aim of the study was to identify cognitive functions and markers which predict preserved memory of the mental health care plan proposed at the emergency department after DSP. Methods: We recruited patients admitted for DSP with BZDs and control patients. At the time of the psychiatric assessment, we performed cognitive tests and we studied the relationship between these tests and the scores of a memory test performed 24 h after. Results: In comparison with the control group, we found memory impairment in the BZD group. We found significant impairment on the Trail Making Test A (TMT A) in the BZD group in comparison with the control group, while TMT A and Wechsler Adult Intelligence Scale (WAIS) Coding test scores were significantly correlated with memory scores. Conclusions: Attentional functions tested by WAIS Coding test and TMT A were correlated with memory score. It could be profitable to assess it in clinical practice prior to a psychiatric interview.
The Autonomous Unit System at the Ontario Hospital, New Toronto: Part 1
Authors: Ray Edward 
Published: April 2017

This paper presents a description and preliminary objective evaluation of a new method of hospital organization. Replacing the traditional centralized scheme of organization the unit system concept involves the division of this hospital into a series of functionally autonomous units with a complete treatment team on each unit. The aim of this scheme was to offer to the patient more concentrated and personal attention. With an awareness of the weaknesses of the historical approach, hospital statistics for the first year of operation under the unit system were compared with those of the previous year. Increases were noted in; the number of patients placed in hospital approved boarding homes, the number of patients placed on probation, and in the discharge rate. A decrease was noted in the average length of stay in hospital before discharge. It is recognized that changes in data reflect not only the effects of the unit system but also the effects of other variables operative at this time. The data presented are suggestive rather than conclusive evidence of the efficiency of the unit system.
A Psychiatric Approach to the Study of Nightmare
Authors: De Verteuil Roger L. 
Published: April 2017

1. Although the nightmare is a common form of dream, and beyond doubt an authentic experience, it has never been adequately explained and in fact still remains to be properly defined. 2. We have attempted here to arrive at some definition of nightmare, and in so doing to sketch a tentative classification of dreams. Examples have been taken from the dreams of patients under treatment, and from the dream-like creations of Edgar Allan Poe. 3. Four types of dreams are briefly described: a. The wish-fulfilling dream, which is the type best known and understood. b. The pipe-dream, an extreme form of wish-fulfilling dream, with certain specific features. c. The nightmare, characterized by chaotic structure and highly disturbing emotions (dread, horror, loathing, disgust) and not adequately explained by any known hypothesis. d. The intuitive dream, in which we find unconscious and apparently instinctive perceptions of truth which are only later available to conscious reasoning. 4. An attempt is made to show in which way these types of dream are distinct from one another, and in which way they are inter-related. 5. Finally, elements common to both the phenomena of nightmare and those of functional psychoses are pointed out, with the suggestion that similar causative mechanisms may be at work in both.
The Essentials of Behaviour Therapy
Authors: Costello C.G. 
Published: April 2017

The following four distinguishing features of behaviour therapy are discussed. a) Neurotic reactions are learned. b) People differ in the speed with which they learn them. c) They may be learned in later periods of life than childhood. d) If the neurotic reaction is eliminated you get rid of the neurosis. In discussion of these features, behaviour therapy is contrasted with psychoanalytic therapy. Cases treated by means of reciprocal inhibition, aversion therapy and negative practice are briefly described. Finally, an attempt is made to answer the critics of behaviour therapy and their main criticisms that: a) With removal of one neurotic symptom a substitute symptom will take its place. b) Personal relationships are ignored. c) The behaviour therapist's technique is too like brain washing. d) Behaviour therapy can deal only with simple symptoms such as tics and writer's cramp.
Overinclusive Thinking in Symptom-Free Schizophrenics
Authors: Payne R.W. , Ancevich Singrida S. , Laverty S.G. 
Published: April 2017

1. Three groups of patients who had recovered from their illness, and who showed virtually no symptoms, were tested. Nearly all had received drug treatment for at least a month, and many were still taking drugs. Of the 54 patients, 16 had been diagnosed as schizophrenic, and had been actively deluded in the past. Seventeen had been diagnosed as schizophrenic, but had not been actively deluded. The remaining 21 had not been regarded as schizophrenic. 2. A previous study, testing exactly similar groups prior to treatment, had found the deluded schizophrenics most overinclusive, the non-deluded schizophrenics slightly overinclusive, and the non-schizophrenics normal in this respect. In the present study, there were no significant differences between the three groups on the measure of overinclusion used, the Object Classification Test. Furthermore the subjects were, for all practical purposes, all within the normal range on this measure when compared with previously published data from normal people. It was therefore concluded that overinclusive thinking in schizophrenia is probably a symptom of the illness, and not a permanent personality characteristic of the individuals concerned. 3. Two new tests of overinclusive thinking, both involving the establishment of a perceptual “set”, were tried out to see if they were practicable. The results were negative in that in neither procedure was any set developed. 4. A measure of abnormal retardation was also used, derived from the Object Classification Test. Again, the three groups were not significantly different, nor did they differ from a previously published normal group. This suggests that abnormal retardation, also, is a symptom of the illness of psychotic patients, and not a permanent personality characteristic.
Ulcerative Colitis — Criteria of a “Psychosomatic” Disease
Authors: Powles William E. 
Published: April 2017

Ulcerative colitis is one of a loose group of “psychosomatic” or “psychophysiologic” diseases appearing together in our present official nosological classification. These illnesses share certain common features: the presence of tangible lesions and pathophysiology, the possibility of serious and fatal outcomes, association with certain mental states, and mediating mechanisms outside the voluntary nervous system. This paper is a discussion of the historical steps or criteria necessary to “establish” a disease entity as “psychosomatic”, illustrated by features of ulcerative colitis, the people who suffer from it, and their treatment. The criteria of a psychosomatic disease, as presented, are: — 1. The association of life stresses with exacerbations of the disease. 2. The finding of generally disturbed personality types associated with sufferers from the disease. 3. Some specificity of personality traits in sufferers from the disease, traits which usually do not fall within any standard psychiatric diagnosis. 4. Some specificity of the type of life stress precipitating attacks of the disease in predisposed people. 5. Establishment of scientifically plausible connections between personality type, specific stress, mental state, and pathophysiologic reaction. 6. Evidence that a specific psychotherapeutic approach contributes to remission, over and above other treatment measures.
Sheltered Workshops
Authors: Houston Frederick 
Published: April 2017

From a mental hospital in England, in 1956, contacts were made with industry to obtain contracts for work to be performed in a hut in the hospital grounds. The manufacturers supplied the material and tools, and a female attendant was appointed as supervisor. Patients were paid for each finished article. The unit was restricted to chronic female patients. Eighty-two patients were studied, 30 of whom had been in hospital for more than a year. Thirty-six of the patients in the project recovered sufficiently to be discharged, of those, 30 who had been hospitalized for more than a year, five were discharged. These five had spent 22, 10, 6 1/2, 4 1/2, and 1 1/2 years respectively in hospital before they went to work in the sheltered workshop. All patients improved. It was felt that such a project supplies reality testing, resocialization, and a monetary incentive to recovery, and that vocational training was not the main factor here. High morale and prestige of those engaged, as in the Hawthorne experiment, were important. Other industrial units in the hospital, e.g. laundry and sewing room, acted as a control to the experiment. It is suggested that such an idea be tried more extensively in Canadian mental hospitals, and that scientific measurements be made of changes produced.
Conditioning Techniques in Psychotherapy
Authors: Burnett Alastair , Ryan Edmund 
Published: April 2017

Over the last decade more and more articles and books have been published dealing with the application of learning theory and principles in the individual and group psychotherapy of neurotic patients. In this paper, a patient population attending the Day-Care Clinic in the Mental Hospital, St. John's, Newfoundland, is described and the application of a learning theory type of therapy is discussed. These patients came mainly from small, isolated fishing villages or out-ports, located around the coast of Newfoundland. Most of them had gone only as far as Grade VII or VIII in school and were unsophisticated regarding their symptomatology and emotional illness. Several studies on normal persons living in out-ports had indicated that their performance abilities are much better developed than their verbal-conceptual ones. It was felt, therefore, that patients of this type might benefit from conditioning and supportive therapy rather than from any sophisticated analytic treatment which would require a fair level of education and ability to verbalize. The results of this type of treatment approach on rural “unsophisticated” patients who have limited formal education suggest that an approach involving conditioning therapy and basic education may be quite useful. Also the results indicate that the emphasis on the psychotherapy of the intelligent urban patient may have resulted in the relative neglect of a fairly large proportion of individuals seeking treatment. It is hoped that a greater interest in these less analytically-exciting patients will result from treatments involving basic learning theory and conditioning principles.