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At least 289 records · Page 16Linked to original sources
PubMed2025

ShortCake: an integrated platform for efficient and reproducible single-cell analysis.

SUMMARY: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple "flavors," enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility. AVAILABILITY AND IMPLEMENTATION: The ShortCake image is available on DockerHub (https://hub.docker.com/r/rnakato/shortcake) and Zenodo (DOIs: 10.5281/zenodo.17116765 and 10.5281/zenodo.17118158). The source code is available on GitHub (https://github.com/rnakato/ShortCake).

Single-Cell Analysis↗
PubMed1996

Computer administration of a school-based adolescent health survey.

OBJECTIVE: To examine the utility of notebook computers in the collection of data in large scale surveys. METHODOLOGY: A notebook computer administered survey of health in adolescents was conducted in 1992 using a multi-instrument questionnaire. Students in school years 7, 9 and 11 in private and government schools in Melbourne and rural Victoria participated. RESULTS: Parental consent was obtained with an 83% response rate. Each student answered questions directly onto the computer taking an average of 68 min to complete the highly branched confidential but not anonymous questionnaire. Students were presented with on average 33% of the 897 possible questions. Over 90% of students reported enjoying using the computer. Those who reported answering the questions honestly all the time ranged from 68 to 85%, increasing with grade level. CONCLUSIONS: The use of computers in survey research provides many advantages in data collection including exposure only to relevant questions and the opportunity of asking sensitive questions.

Adolescent↗
PubMed1979

Investigation of hot flashes by ambulatory monitoring.

The unpredictability of hot flashes makes their investigation difficult. A method for continuous monitoring of subjective arousals and their objective correlates is here described and illustrated with results from one subject. Temperatures of special interest with respect to hot flashes--toe, cheek, vagina, and air--were recorded on a protable magnetic tape during routine living at home. The subject signaled the "on" and "off" of each perceived flash with a hand switch and also entered information in a notebook. She signaled 63 flashes on 5 days, during which the cheek and toe temperatures showed transient increments. Some of the flashes were labeled uncertain in the notebook. The subject also had 23 episodes of these temperature increments that she did not identify by signals as flashes. In these episodes, therefore, the mechanism of consciousness was not activated. Perceptions that coincided with transient temperature increments thus ranged as follows: subconscious, uncertain, definite but bearable, mildly distressful, and strongly distressful. Hence ambulatory monitoring can provide objective evidence of transient activation of the hypothalamic heat loss mechanism, whether perceived or not.

Body Temperature↗
PubMed2006

Mobile education in autopsy conferences of pathology: presentation of complex cases.

BACKGROUND: MeduMobile was a project to develop and evaluate learning scenarios for medical students and teachers by use of video communication and notebooks. Its core part was assigned to various medical routines, conferences or meetings such as doctor-patient bedside conversation. These were filmed by video teams and broadcasted live via the WLAN of the Charité campus to course participating students. One type of the learning arrangements was the autopsy conference as an on-call scenario. MATERIALS AND METHODS: The MeduMobile project consisted of two main compartments: the regular seminar event which took place every week or month, and the on-call event. For an on-call event the students were informed two hours before the lesson's start. A mobile video team organised the video conference via a specific MeduMobile seminar system. This software offered the students to log. The MeduMobile seminar system is based on the Windows operating system and realises an extended video communication via WLAN. Thirteen access points were implemented at the Charité Campus Virchow Klinikum and Campus Mitte. A questionnaire was developed to investigate in the response and learning effect of the mobile seminar system. RESULTS: During the MeduMobile project 42 video conferences with (cumulative) 145 participating students took place. Four autopsy conferences could be organised as on-call scenarios within this project. A prospective, not randomised follow-up study was included 25 students of the 1st - 6th clinical semester. According to the answers, professional reasoning, professional performance, sustainability, and the complexity were broadly accepted by the students. DISCUSSION: In principle, the MeduMobile realised an interdisciplinary case presentation using video conference and web page. The evaluation indicates a high acception of such complex case presentation with multidisciplinary settings. The use of the notebooks in mobile learning enables an interconnective training and promotes a complex learning.

Journal Article↗
PubMed2004

Mustafa Sakarya (1901-1988): Turkish fellow of Walter E. Dandy.

Walter E. Dandy is one of the true pioneers of modern neurosurgery. This eminence led many surgeons to visit his department for training. Mustafa Sakarya, a Turkish surgeon, was Dr. Dandy's only fellow from Turkey. He spent 9 months at the Johns Hopkins Hospital and wrote his observations in a notebook during this period. The notebook contains information regarding the patients, operative schedules, and surgical techniques, as well as theoretical reviews. His notes are of potential interest to both American and Turkish neurosurgeons.

Fellowships and Scholarships↗
PubMed2002

Fleming's Unfinished.

It is often suggested that, soon after he discovered penicillin, Alexander Fleming lost interest in what became the most important of all the antibiotics. Fleming's notebooks, however, show that he continued working with penicillin throughout the 1930s, even to the point when Florey and Chain became interested in it. During this period, Fleming isolated new airborne molds and checked them for their ability to produce antibacterial agents, and he also investigated other examples of microbial antagonism, such as bacteriophages. Unfortunately, none of this work was published. What follows is a simulation, based largely upon Fleming's notebooks, of a paper that he might have written in early 1940. This version of "Fleming's Unfinished" should once and for all dismiss the view that he failed fully to recognize the significance of his famous discovery.

Bacteria↗
PubMed2002

A glance back in time: the nursing notes of Edwina Perkins.

Edwina Perkins was a student nurse in South Wales between 1937 and 1941. This article reviews her nursing notebooks, their context and relation to current practice. The notebooks are examined with regard to their historical contribution, enhancing insights into nursing past and present, and, from a more personal perspective, Edwina's life as a nurse and the process of discovering more about her.

History, 20th Century↗
PubMed1992

[The use of narcotic analgesics in primary care in Spain (1988-1991). An evaluation of the impact of new technologies in the pharmaceutical sector].

OBJECTIVE: To analyse the results of the policy of encouraging rational use of analgesics in Spain. DESIGN: Longitudinal retrospective and observational study, on the exhaustive information deriving from the filling out of Analgesic Extra-therapeutic Dose notebooks. SITE. Primary Care treatment of terminal oncological patients carried out basically in the Province of Barcelona. PARTICIPANTS: All treatments carried out under the extra-therapeutic dose notebook during the last quarter of 1988 and the first quarters of 1989, 1990, and 1991. MAIN MEASUREMENTS AND RESULTS: Revision of initial treatment, change of medication and posology and returns on the basis of the extensive documentation generated. Consumption has risen from 157 authorized cases in 1989 to 404 in 1991. CONCLUSIONS: Consumption has increased sharply, although the opinion that such analgesics are under-used still predominates. Along with the quantitative increase there has been a corresponding deterioration in the rationale informing use and control, both medically (patterns of treatment, excesses) and socially (cost effectiveness, fair allocation). The evaluation in force before the advent of new technology and policies should be reinstated if we wish to achieve the desired level of effectiveness, adapting national health care by coordinating social and health care and bringing up to standard the training and supply of information to health workers. It is suggested that a "Consensus" Conference should be organised to bring up to date the basis on which analgesics are used and regulated.

Analgesics, Opioid↗
PubMed1989

Tallow and the time capsule: Claude Bernard's discovery of the pancreatic digestion of fat.

In 1848, Claude Bernard discovered that pancreatic secretion could emulsify and saponify fatty substances. He would eventually attribute these reactions to an enzyme that was later named 'pancreatic lipase'. This essay has three goals: 1) to examine Bernard's previously overlooked research on the pancreas; 2) to explore the equally ignored history of lipid digestion and metabolism; 3) to reconstruct Bernard's discovery of pancreatic lipase through a parallel analysis of his laboratory notebooks and his publications. This method reveals a discrepancy between the sequence and motivation of events as they were reported by Bernard in his publications and as they appear in his laboratory notebooks.

Animals↗
PubMed1996

[Ambulatory follow-up in oral anticoagulation: recommendations for clinical practice].

The aim of this investigation performed in 75 outpatients taking oral anticoagulant after an episode of pulmonary embolism was to specify the modalities of ambulatory monitoring during oral anticoagulation. All patients were followed up by their family doctor after hospital discharge. The principal results of this investigation were (1) the general difficulty of obtaining and maintaining anticoagulation stability in a recommended therapeutic range (INR 2-3) for venous thromboembolic disease, (2) that in only 15% of personal anticoagulation notebooks were the laboratory results expressed in INR, (3) the lack of information given to the patients taking oral anticoagulant. Based on these results we started an education programme for nurses and physicians designed to promote the use of INR and to improve the quality of information given to anticoagulated patients. A new anticoagulation monitoring notebook should help medical staff and patients to increase the safety of anticoagulation.

Administration, Oral↗
PubMed1977

Computer program for maintenance of individual animal records in a nonhuman primate colony.

A computer program was developed to maintain animal records for a nonhuman primate colony used in research. The program was designed for use with an existing laboratory notebook system. The computer program identifies each notebook entry containing information about each animal and keeps other information, including animal name, sex, species, projects to which the animal is assigned, location of the animal, dates and body weights. The program is interactive and easy to use. Information stored in the system is readily accessible to all investigators using the animals. In 17 months of use, 1382 master file entries were developed for 113 monkeys.

Animals↗
PubMed1998

An assessment of the 'road-to-health' card based on perceptions of clinic staff and mothers.

OBJECTIVES: To describe the opinions of health personnel and parents at child health clinics in Cape Town; to determine the accuracy and completeness of data recorded on the present 'Road-to-Health' (RTH) card; and to ascertain the views of clinic staff and mothers regarding what information they would like to record. DESIGN: Descriptive prospective study. SETTING AND SUBJECTS: Qualitative interviews of 35 health personnel and 150 mothers/caregivers were conducted at 17 child health clinics. The clinic practices of 32 health personnel were monitored and details of 150 RTH cards were examined. MAIN OUTCOME MEASURES: Responses of health personnel at public and private child health clinics and of mothers were analysed. Data recorded on the card were extracted under the headings: neonatal data, immunisation schedules, measurements, and weight-for-age chart. RESULTS: Most nurses supported the concept of an RTH card but a large majority recommended that it be replaced with a notebook retained by the mother. A significant proportion of health personnel did not know how to use the weight-for-age chart. Most mothers attending clinics carried the card, but this number dropped for hospital visits and consultations with private doctors. Mothers' understanding of the card was limited. For mothers the weight-for-age chart, immunisation schedule and milestone section are obscure. CONCLUSION: Health personnel and mothers would like to replace the RTH card with a notebook in the parents' home language. It should contain more information on health matters, adequate space to record weight and infectious diseases, an illustrated milestone chart and an improved schedule for immunisations. Mothers perceived the RTH card as belonging to the clinic and wanted a 'baby's own' document.

Attitude of Health Personnel↗
PubMed1996

The branched eating disorders test: validity in a nonclinical population.

OBJECTIVE: To develop an effective measure of the symptoms of eating disorders for use in community surveys. METHOD: A branched eating disorders instrument for administration by notebook computer was evaluated as a screen in 487 teenage schoolgirls. High scorers and a stratified sample of low scorers were evaluated in a second-stage interview with the Eating Disorders Examination (EDE). RESULTS: The Branched Eating Disorders Test (BET) proved to have exceptional validity coefficients (sensitivity 100%, specificity 99%, positive predictive value 70%). DISCUSSION: This pilot validation suggests that the BET largely overcomes the problems of earlier instruments of limited screening utility when applied to community samples.

Adolescent↗
PubMed1997

Charles Darwin as primatologist: a literature guide.

Charles Darwin made numerous references to the nonhuman primates in support of his evolutionary thesis. Most such references are found in The Descent of Man [1871] and The Expression of the Emotions in Man and Animals [1872], but other illuminating statements are scattered throughout Darwin's notebooks, letters, and lesser-known publications. As a research aid to modern primatologists, this paper presents a very nearly complete listing of Darwin's comments on primates, indexed by topic and primate type.

Animal Communication↗
PubMed1988

Laboratory use of the personal computer: a program in MS-DOS BASIC, for generating specimen labels and data sheets for electron microscopy.

Conventionally, all specimen vial and block labels are handwritten or typed, a labor-intensive process open to human error, particularly in a lab that processes large numbers of samples. The computer program described in this report was developed to reduce or eliminate this problem. The program is menu-driven, asking specific information from the user, and runs on an IBM PC (or compatible). It is designed to accurately produce specimen collection vial labels, resin block labels, and data sheets for inclusion in a research notebook. A task that in the past may have required much time at the typewriter can now be accomplished without error in a few minutes. Although designed to fit the needs of a pathology laboratory, the program (written in BASIC) can be easily modified to fit other applications.

Microcomputers↗
PubMed1992

Computer-assisted morphometry: point, intersection, and profile counting and three-dimensional reconstruction.

The use of computers in morphometry can involve 1) automated image analysis, semiautomated image analysis and point, intersection, intercept and profile counts of two-dimensional images on tissue sections with mathematical extrapolation to the third dimension, 2) direct measurement of volumes, surfaces, lengths, and curvature using x,y,z coordinates of serial sectioned images, or 3) stereologic techniques and serial sections which is a combination of 1 and 2 above. Automated and semiautomated image analysis are generally restricted to specimens that are characterized by differential contrast such as interalveolar septa in the lung or histochemically stained mucous granules in pulmonary epithelium. Point, intersection, and profile counts using hand-held, notebook PCs, portable PCs, or standard PCs and MS-DOS-based application programs are extremely efficient, precise, affordable, and convenient methods of quantitating average values of a population. When morphometric measurements of individual structures are required, computer-assisted three-dimensional reconstruction using x,y,z coordinates of the surface outline from serial sections is a tedious yet precise method. We describe a computer program that efficiently estimates mean caliper diameter, volume, and surface area with less than five percent error with five sections per structure. We also describe a program that does digital image subtraction on serial sections, superimposes digitally generated test systems on biological images, and accumulates point, intersection, and profile counts using a Macintosh II series computer.

Animals↗
PubMed1994

A new device for ambulatory cough recording.

Nocturnal cough reporting on diary cards has been shown to be unreliable and inconsistent. Whether subjective reporting of daytime cough is equally unreliable remains unknown. We have, therefore, developed a new and easily portable device (RBC-7) that records electromyographic (EMG) and audio cough signals for at least a 24-hr period, with a capacity of over 48 hr. Additional information is obtained from electrocardiographic (ECG) signals, and from an accelerometer indicating the level of the subject's activity. The RBC-7 can be set up with the aid of a notebook computer at the subjects home, school or workplace. Initial studies utilizing a prototype device were performed to determine the optimal position of the EMG leads and the microphone. The optimal position for the EMG leads was determined as the positive electrode in the sixth intercostal space (ICS) in the midclavicular line on the left, the negative electrode in the same position on the right, and the reference electrode in the midline over the abdomen. This position was shown to give the highest EMG voltages and the greatest difference in voltages between cough and other signals. The optimal microphone position for signal strength and comfort was over the first ICS, either right or left, close to the sternum. Recordings were performed simultaneously in 20 subjects with conventional tape recorders and the multiparametric cough monitoring system (RBC-7). Conventional tape recordings limited the duration of the studies due to the inherent restrictions. No significant difference in the number of single coughs recorded by each system was detected (correlation coefficient = 0.996). The RBC-7 offers a unique opportunity to obtain objective information on cough in ambulatory subjects over at least a 24-hr period, and to relate cough to time, activity and heart rate, while normal activities are pursued.

Adult↗