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Open Access Publications from the University of California

Scholarly Works (25 results)

  • Article
UC Berkeley Previously Published Works (2011)
    Cover page: Python for Scientists and Engineers
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)
    Parental expressed emotion (EE) attitudes are important prognostic indicators in the course of bipolar disorder (BD) in adolescents and adults. This study examined the hypothesis that parents' own susceptibility to affective disturbances contributes to their likelihood of high-EE attitudes. We examined past-week levels of emotional distress, lifetime affective diagnoses, and family histories of affective disorder among high- and low-EE parents of 86 adolescents with bipolar I or II disorder who were recovering from an episode of depression or (hypo) mania. High EE parents endorsed higher concurrent levels of depression, anxiety, and anger/hostility than low EE parents, and reported a greater familial history of depression and BD. No differences between high and low EE parents were found in concurrent levels of interpersonal sensitivity, lifetime rates of affective disorders, or familial loading of anxiety disorder. Parents' distress at the time of the EE assessment was the strongest correlate of EE. The results suggest that susceptibility to affective psychopathology may be an important contributor to the development of EE attitudes among parents of adolescents with BD.
      Cover page: Expressed emotion, emotional distress, and individual and familial history of affective disorder among parents of adolescents with bipolar disorder
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      • Peer Reviewed
      UC Berkeley Previously Published Works (2018)
      We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MR scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science.
        Cover page: Teaching Computational Reproducibility for Neuroimaging.
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2023)
        Spatial abilities of hens are particularly sensitive to development during early life. Experiences in pullet housing may have lasting consequences on adult hens movements in cage-free environments. We tested whether opportunities to access elevated spaces during rearing improved hens use of a multitiered aviary. Female Dekalb White pullets were reared in either floor pens (FL), single-tiered aviaries (ST), or 2-tiered aviaries (TT; n = 5 pens/environment) through 16 wk of age. Rearing structures were replaced with identical multitiered aviaries at 17 wk. The distribution of the flock within the aviary and the vertical transitions of 10 focal hens/pen across the aviary were determined from videos recorded during their first (D1) and seventh (D7) day of aviary access, as well as at 19, 23, and 27 wk of age. Prevalence of floor eggs was recorded weekly from 17 to 28 wk of age. On D1, more ST and TT hens utilized the aviary during the daytime (P = 0.0077), made more vertical transitions when searching for a roosting spot in the evening (P = 0.0021), and maintained a consistent distance traveled during transitions compared to FL hens (P = 0.02). These differences disappeared by D7, except that ST and TT hens continued to roost on the highest perches of the aviary more (P < 0.0001) than FL hens through 27 wk of age. FL hens laid more floor eggs than ST and TT hens for the first 2 wk of lay (P < 0.0001). The majority (97.9%) of vertical transitions was controlled. Uncontrolled transitions were highest at D1 and decreased by D7 (P = 0.0009) and were not affected by rearing (P = 0.33). The results suggest that hens reared with minimal height are hesitant to use the laying hen aviaries when they are first transferred. They acclimate within 1 to 2 wk, but continue to roost less in the highest accessible level.
          Cover page: Providing elevated structures in the pullet rearing environment affects behavior during initial acclimation to a layer aviary.
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2013)
          Background: Respiratory isolation of inpatients during evaluation for TB is a slow and costly process in low-burden settings. Xpert MTB/RIF (Xpert) is a novel molecular test for tuberculosis (TB) that is faster and more sensitive but substantially more exp
            • Article
            • Peer Reviewed
            Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 16, Issue 1 (2015)

            Introduction: The most effective use of trauma center resources helps reduce morbidity and mortality, while saving costs. Identifying critical infrastructure characteristics, patient characteristics and staffing components of a trauma center associated with the proportion of patients needing major trauma care will help planners create better systems for patient care.

            Methods: We used the 2009 National Trauma Data Bank-Research Dataset to determine the proportion of critically injured patients requiring the resources of a trauma center within each Level I-IV trauma center (n=443). The outcome variable was defined as the portion of treated patients who were critically injured. We defined the need for critical trauma resources and interventions (“trauma center need”) as death prior to hospital discharge, admission to the intensive care unit, or admission to the operating room from the emergency department as a result of acute traumatic injury. Generalized Linear Modeling (GLM) was used to determine how hospital infrastructure, staffing Levels, and patient characteristics contributed to trauma center need.

            Results: Nonprofit Level I and II trauma centers were significantly associated with higher levels of trauma center need. Trauma centers that had a higher percentage of transferred patients or a lower percentage of insured patients were associated with a higher proportion of trauma center need.  Hospital infrastructure characteristics, such as bed capacity and intensive care unit capacity, were not associated with trauma center need. A GLM for Level III and IV trauma centers showed that the number of trauma surgeons on staff was associated with trauma center need.

            Conclusion: Because the proportion of trauma center need is predominantly influenced by hospital type, transfer frequency, and insurance status, it is important for administrators to consider patient population characteristics of the catchment area when planning the construction of new trauma centers or when coordinating care within state or regional trauma systems. [West J Emerg Med. 2015;16(1):–0.]

              Cover page: Trauma Center Staffing, Infrastructure, and Patient Characteristics that Influence Trauma Center NeedCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2017)
              Earth's magnetic field, one of the most enigmatic physical phenomena of the planet, is constantly changing on various time scales, from decades to millennia and longer. The reconstruction of geomagnetic field behavior in periods predating direct observations with modern instrumentation is based on geological and archaeological materials and has the twin challenges of (i) the accuracy of ancient paleomagnetic estimates and (ii) the dating of the archaeological material. Here we address the latter by using a set of storage jar handles (fired clay) stamped by royal seals as part of the ancient administrative system in Judah (Jerusalem and its vicinity). The typology of the stamp impressions, which corresponds to changes in the political entities ruling this area, provides excellent age constraints for the firing event of these artifacts. Together with rigorous paleomagnetic experimental procedures, this study yielded an unparalleled record of the geomagnetic field intensity during the eighth to second centuries BCE. The new record constitutes a substantial advance in our knowledge of past geomagnetic field variations in the southern Levant. Although it demonstrates a relatively stable and gradually declining field during the sixth to second centuries BCE, the new record provides further support for a short interval of extreme high values during the late eighth century BCE. The rate of change during this "geomagnetic spike" [defined as virtual axial dipole moment > 160 ZAm2 (1021 Am2)] is further constrained by the new data, which indicate an extremely rapid weakening of the field (losing ∼27% of its strength over ca. 30 y).
                Cover page: Six centuries of geomagnetic intensity variations recorded by royal Judean stamped jar handles
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2014)

                Background

                Placing inpatients with presumed active pulmonary tuberculosis in respiratory isolation pending results of serial sputum acid-fast bacilli (AFB) smear microscopy is standard practice in high-income countries. However, this diagnostic strategy is slow and yields few tuberculosis diagnoses. We sought to determine if replacing microscopy with the GeneXpert MTB/RIF (Xpert) nucleic acid amplification assay could reduce testing time and usage of isolation rooms.

                Methods

                We prospectively followed inpatients at San Francisco General Hospital undergoing tuberculosis evaluation. We performed smear microscopy and Xpert testing on concentrated sputum, and calculated diagnostic accuracy for both strategies in reference to serial sputum mycobacterial culture. We measured turnaround time for microscopy and estimated hypothetical turnaround times for Xpert on concentrated and unconcentrated sputum. We compared median and total isolation times for microscopy to those estimated for the 2 Xpert strategies.

                Results

                Among 139 patients with 142 admissions, median age was 54 years (interquartile range [IQR], 43-60 years); 32 (23%) patients were female, and 42 (30%) were HIV seropositive. Serial sputum smear microscopy and a single concentrated sputum Xpert had identical sensitivity (89%; 95% confidence interval [CI], 52%-100%) and similar specificity (99% [95% CI, 96%-100%] vs 100% [95% CI, 97%-100%]). A single concentrated sputum Xpert could have saved a median of 35 hours (IQR, 24-36 hours) in unnecessary isolation compared with microscopy, and a single unconcentrated sputum Xpert, 45 hours (IQR, 35-46 hours).

                Conclusions

                Replacing serial sputum smear microscopy with a single sputum Xpert could eliminate most unnecessary isolation for inpatients with presumed tuberculosis, greatly benefiting patients and hospitals.
                  Cover page: Impact of GeneXpert MTB/RIF Assay on Triage of Respiratory Isolation Rooms for Inpatients With Presumed Tuberculosis: A Hypothetical Trial
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2014)
                  We examined the role of innate cells in acquired resistance to the natural murine parasitic nematode, Nippostrongylus brasiliensis. Macrophages obtained from lungs as late as 45 d after N. brasiliensis inoculation were able to transfer accelerated parasite
                    • Article
                    • Peer Reviewed
                    UCSF Open Access Publishing Fund (2013)
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