Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Utility of Plasma Procalcitonin for Nosocomial Pneumonia in the Intensive Care Unit Setting

BACKGROUND: Nosocomial pneumonia is a difficult diagnosis to establish in the intensive care unit setting, due to the non-specific nature of the clinical and radiographic findings. Procalcitonin is a circulating biomarker that may become elevated in the presence of bacterial infection. METHODS: We conducted a prospective single-center cohort study at Barnes-Jewish Hospital, a 1,200-bed urban teaching hospital in St Louis, Missouri. In medical and surgical intensive care unit patients with suspected nosocomial pneumonia we measured plasma procalcitonin with an enzyme-linked fluorescent assay. RESULTS: We evaluated 104 consecutive patients with suspected nosocomial pneumonia, 67 (64%) of whom met our predefined clinical and microbiologic criteria for definite nosocomial pneumonia. Though the mean procalcitonin concentration was greater in the 67 patients with definite nosocomial pneumonia (18.3 ± 99.1 ng/mL, median 0.8 ng/mL, 5th percentile 0.0 ng/mL, 95th percentile 43.1 ng/mL) than in the 12 patients with definite absence of nosocomial pneumonia (1.7 ± 2.0 ng/mL, median 1.0 ng/mL, 5th percentile 0.0 ng/mL, 95th percentile 6.7 ng/mL), this difference was not statistically significant (P = .66). A procalcitonin cutoff value of > 1 ng/mL yielded a diagnostic sensitivity of 50% and a specificity of 49% for definite nosocomial pneumonia. Receiver operating curve and multivariate logistic regression analyses demonstrated that procalcitonin is inferior to clinical variables for diagnosing nosocomial pneumonia. However, compared to patients with an initial procalcitonin > 1 ng/mL, those with lower procalcitonin had fewer total antibiotic days (13.0 ± 10.3 d vs 19.7 ± 12.0 d, P < .001) and fewer antibiotic days for treatment of nosocomial pneumonia (10.0 ± 5.9 d vs 14.7 ± 7.4 d, P < .001). CONCLUSIONS: Plasma procalcitonin has minimal diagnostic value for nosocomial pneumonia.
Living Donor Liver Transplantation for Hepatocellular Carcinoma: Tokyo University Series

Background/Aims: Hepatocellular carcinoma (HCC) is one of the major indications for living donor liver transplantation (LDLT). Unlike in deceased donor liver transplantation, however, there exist no universally adopted selection criteria for the potential candidates with HCC in LDLT. Our institutional guideline for HCC in LDLT has been up to 5 nodules with a maximum diameter of 5 cm (5-5 rule). Methods: A total of 78 adult patients underwent adult living donor liver transplantation at University of Tokyo between April 1996 and October 2005. Results: Overall and recurrence-free survival at 5 years after transplantation were 75 and 90%, respectively, with a median follow-up of 2 years. When stratified by the 5-5 rule, recurrence-free survival at 3 years for patients fulfilling the criteria and those exceeding the criteria was 94 and 50%, respectively. Conclusions: In LDLT, the indication for HCC might be expanded from the Milan criteria, with equivalent outcomes. Further study, however, is necessary to justify the general application of the 5-5 rule.
Tumor Spectrum in ARF-deficient Mice 1

The p19 product of the INK4a/ARF locus is induced in response to potentially oncogenic hyperproliferative signals and activates p53 by interfering with its negative regulator, Mdm2. Mice lacking ARF are highly prone to tumor development, and in this study, 80% of these animals spontaneously developed tumors and died within their first year of life. Mice that were heterozygous for ARF also developed tumors after a longer latency, whereas their wild-type littermates did not. In heterozygotes, tumor formation was accompanied by loss of the residual ARF allele and/or lack of ARF mRNA expression, implying that ARF can act as a canonical “two-hit” tumor suppressor gene. Tumors occurred earlier in life in ARF-null animals that were neonatally irradiated or given dimethylbenzanthrene, and several animals treated with carcinogen simultaneously developed multiple forms of malignancy arising from distinct cell lineages. Although p53-null mice primarily develop lymphomas and fibrosarcomas, the frequency of these two tumor types was inverted in ARFnull animals, with undifferentiated sarcomas predominating in a 3:2 ratio; 28% of ARF-null animals developed carcinomas and tumors of the nervous system, which have been rarely observed in untreated p53-null mice. The longer latency of tumor formation in ARF-null versus p53-null mice, therefore, appears to enable a broader spectrum of tumors to emerge.
The Power of Environmental Observatories for Advancing Multidisciplinary Research, Outreach, and Decision Support: The Case of the Minnesota River Basin

Observatory‐scale data collection efforts allow unprecedented opportunities for integrative, multidisciplinary investigations in large, complex watersheds, which can affect management decisions and policy. Through the National Science Foundation‐funded REACH (REsilience under Accelerated CHange) project, in collaboration with the Intensively Managed Landscapes‐Critical Zone Observatory, we have collected a series of multidisciplinary data sets throughout the Minnesota River Basin in south‐central Minnesota, USA, a 43,400‐km2 tributary to the Upper Mississippi River. Postglacial incision within the Minnesota River valley created an erosional landscape highly responsive to hydrologic change, allowing for transdisciplinary research into the complex cascade of environmental changes that occur due to hydrology and land use alterations from intensive agricultural management and climate change. Data sets collected include water chemistry and biogeochemical data, geochemical fingerprinting of major sediment sources, high‐resolution monitoring of river bluff erosion, and repeat channel cross‐sectional and bathymetry data following major floods. The data collection efforts led to development of a series of integrative reduced complexity models that provide deeper insight into how water, sediment, and nutrients route and transform through a large channel network and respond to change. These models represent the culmination of efforts to integrate interdisciplinary data sets and science to gain new insights into watershed‐scale processes in order to advance management and decision making. The purpose of this paper is to present a synthesis of the data sets and models, disseminate them to the community for further research, and identify mechanisms used to expand the temporal and spatial extent of short‐term observatory‐scale data collection efforts.
Posttraumatic stress disorder under ongoing threat: a review of neurobiological and neuroendocrine findings

Background Although numerous studies have investigated the neurobiology and neuroendocrinology of posttraumatic stress disorder (PTSD) after single finished trauma, studies on PTSD under ongoing threat are scarce and it is still unclear whether these individuals present similar abnormalities. Objective The purpose of this review is to present the neurobiological and neuroendocrine findings on PTSD under ongoing threat. Ongoing threat considerably affects PTSD severity and treatment response and thus disentangling its neurobiological and neuroendocrine differences from PTSD after finished trauma could provide useful information for treatment. Method Eighteen studies that examined brain functioning and cortisol levels in relation to PTSD in individuals exposed to intimate partner violence, police officers, and fire fighters were included. Results Hippocampal volume was decreased in PTSD under ongoing threat, although not consistently associated with symptom severity. The neuroimaging studies revealed that PTSD under ongoing threat was not characterized by reduced volume of amygdala or parahippocampal gyrus. The neurocircuitry model of PTSD after finished trauma with hyperactivation of amygdala and hypoactivation of prefrontal cortex and hippocampus was also confirmed in PTSD under ongoing threat. The neuroendocrine findings were inconsistent, revealing increased, decreased, or no association between cortisol levels and PTSD under ongoing threat. Conclusions Although PTSD under ongoing threat is characterized by abnormal neurocircuitry patterns similar to those previously found in PTSD after finished trauma, this is less so for other neurobiological and in particular neuroendocrine findings. Direct comparisons between samples with ongoing versus finished trauma are needed in future research to draw more solid conclusions before administering cortisol to patients with PTSD under ongoing threat who may already exhibit increased endogenous cortisol levels. Highlights of the article We reviewed the neurobiological and neuroendocrine findings in PTSD under ongoing threat. PTSD under ongoing threat demonstrated similar brain abnormalities as PTSD after finished trauma. Several studies found increased cortisol levels in PTSD under ongoing threat. Hydrocortisone administration might not be beneficial for individuals with PTSD under ongoing threat with elevated endogenous cortisol levels. Direct comparisons between ongoing versus finished trauma are needed to provide robust conclusions and clinical recommendations.
The distinctive character of lumpy limestones (Early Jurassic, Lusitanian Basin, W Portugal)

Ephemeral carbonate facies presenting restricted geographical and temporal occurrence hold the key to complete the knowledge of past environmental conditions. Far from representing environments widespread throughout the geological history, ephemeral lithofacies embody equally relevant but more unusual scenarios. This is the case of the lumpy limestones, a puzzling facies encased on a worldwide‐relevant stratigraphic section of the Portuguese Jurassic archive but still lacking a deeper understanding of the processes leading to their development. An extensive revision and update of the singularities of the lumpy limestones is presented, based on a systematic description of the lithic elements occurring in three sections. These represent different positions along the Pliensbachian (Early Jurassic) paleoplatform of the Lusitanian Basin (Western Portugal). The lumps were analysed regarding their abundance, distribution, appearance, and degree of sorting, based on field observation, macro‐ and microfacies inspection. Apart from shared stratigraphic trends, which highlight prevailing paleoenvironmental conditions during the Early Jurassic times, the main differences in spatial distribution across the Lusitanian Basin are also discussed, taking into account the specific paleogeographic setting of each studied locality. The presence of lumps but also absence is considered relevant, as for each case a specific paleoenvironmental context and/or syn‐ to post‐depositional processes can be assigned. A new lump classification scheme is brought forward, accounting for the high variety identified in lump architecture and aspect. A depositional model offering alternative paleoenvironmental scenarios is presented for the development of the variety of lump types identified, combining physical (mechanical) and biological processes involved in the occurrence and distribution of this facies. Depending on the presence/absence of lumps, lump type, abundance, and distribution, these scenarios include considerable fluctuations in oxygen availability and bottom current intensity, which affect deposition/accumulation, bioturbation, and related syn‐sedimentary conditions. Physical and mechanically dominated processes driven by sedimentary instability and/or heterogeneity are also introduced. A dynamic depositional framework is presented, clarifying the depositional to late‐diagenetic evolution accounting for the singularity of the lumpy limestone facies in the context of the Lower Jurassic in the western Iberia margin.
PARSEC 2.0: A New Benchmark Suite for Chip-Multiprocessors

The second version of the Princeton Application Repository for Shared-Memory Computers (PARSEC) has been released. PAR-SEC is a benchmark suite for Chip-Multiprocessors (CMPs) that focuses on emerging applications. It includes a diverse set of work-loads from different domains such as interactive animation or systems applications that mimic large-scale commercial workloads. The next version of PARSEC features several improved and one new workload. It also supports an additional parallelization model. Many patches and changes were included which simplify the use of PARSEC in practice. The benchmarks of the new suite have higher scalability and cover a larger number of emerging applications. In this paper we discuss the major changes in detail and provide the information necessary to interpret results obtained with PARSEC 2.0 correctly.
Algorithms to Take Advantage of Hardware Prefetching

Cache-oblivious and cache-aware algorithms have been developed to minimize cache misses. Some of the newest processors have hardware prefetching where cache misses are avoided by predicting ahead of time what memory will be needed in the future and bringing that memory into the cache before it is used. It is shown that hardware prefetching permits the standard Floyd-Warshall algorithm for all-pairs shortest paths to outperform cache-oblivious and cache-aware algorithms. A simple improvement to the standard simple dynamic programming algorithm yields an algorithm that takes advantage of prefetching, and outperforms cache-oblivious and cache-aware algorithms. Finally, it is shown that variants of standard FFT algorithms exhibit good prefetching performance.
Red Cell Distribution Width and Outcome in Patients With Septic Shock

Introduction: Red cell distribution width (RDW) is reflective of systemic inflammation. The objective of this study was to investigate the association between RDW (on day 1 of development of septic shock) and mortality. Methods: A total of 279 patients with septic shock were included. We categorized the patients into quintiles based on RDW as follows: <13.5%, 13.5% to 15.5%, 15.6% to 17.5%, 17.5% to 19.4%, and >19.4%. Results: Red cell distribution width was a strong predictor of hospital mortality with a significant risk gradient across RDW quintiles after multivariable adjustment: RDW 13.5% to 15.5% (odds ratio [OR], 4.6; 95% confidence interval [CI], 1.0-23.4; P = .06); RDW 15.6% to 17.5% (OR, 8.0; 95% CI, 1.5-41.6; P = .01); RDW 17.6% to 19.4% (OR, 25.3; 95% CI, 4.3-149.2; P < .001); and RDW >19.4% (OR, 12.3; 95% CI, 2.1-73.3; P = .006), all relative to patients with RDW <13.5%. Similar significant robust associations were present for intensive care unit mortality. Estimating the receiver–operating characteristic area under the curve (AUC) showed that RDW has very good discriminative power for hospital mortality (AUC = 0.74). The AUC was 0.69 for Acute Physiologic and Chronic Health Evaluation II (APACHE II) and 0.69 for sequential organ failure assessment (SOFA). When adding RDW to APACHE II, the AUC increased from 0.69 to 0.77. Conclusions: Red cell distribution width on day 1 of septic shock is a robust predictor of mortality. The RDW is inexpensive and commonly measured. The RDW fared better than either APACHE II or SOFA, and the sum of RDW and APACHE II was a stronger predictor of mortality than either one alone.
High Expression of Protein Tyrosine Kinase 7 Significantly Associates with Invasiveness and Poor Prognosis in Intrahepatic Cholangiocarcinoma

Background The incidence, prevalence, and mortality of intrahepatic cholangiocarcinoma (ICC) are increasing worldwide. Protein tyrosine kinase-7 (PTK7) is upregulated in many common human cancers. However, its expression in ICC has not been studied. The present study aimed to explore the underlying mechanism of PTK7 in ICC. Materials and Methods The role of PTK7 was studied in vitro by suppressing PTK7 expression in ICC cell lines. The in vivo effect of PTK7 was evaluated using a nude mouse model inoculated with a human ICC cell line. We also examined the role of PTK7 in human ICC samples. Results Cells with high PTK7 expression exhibited higher proliferation, DNA synthesis, invasion, and migration abilities than did cells with low PTK7 expression. The knockdown of PTK7 with small interfering RNA (siRNA) in high PTK7 expressing cells resulted in impairment of invasion, migration, and DNA synthesis through the regulation of several cell-cycle-related proteins. It also induced cell apoptosis and decreased phospho-RhoA expression. In a xenograft nude mouse model, PTK7 siRNA resulted in a reduction of the tumor size, compared with scrambled siRNA injection. PTK7 expression was higher in human ICC than in the normal bile duct. Patients with low expression of PTK7 had a longer disease-free survival and overall survival than those with high expression. Conclusions PTK7 expression plays an important role in the invasiveness of ICC cells and leads to a poor prognosis in ICC patients. Thus, PTK7 can be used as a prognostic indicator, and the inhibition of PTK7 expression could be a new therapeutic target for ICC.
Seasonal and Diurnal Variations in Atmospheric and Soil Air 14CO2 in a Boreal Scots Pine Forest

Abstract We present a radiocarbon (14C) dataset of tropospheric air CO2, forest soil air CO2, and soil CO2 emissions over the course of one growing season in a Scots pine forest in southern Finland. The CO2 collection for 14C accelerator mass spectrometry (AMS) analysis was done with a portable, suitcase-sized system, using molecular sieve cartridges to selectively trap CO2. The piloting measurements aimed to quantify the spatial, seasonal and diurnal changes in the 14C content of CO2 in a northern forest site. The atmospheric samples collected above the canopy showed a large seasonal variation and an 11‰ difference between day and nighttime profiles in August. The higher Δ14C values during night are partly explained by a higher contribution of 14C-elevated soil CO2, accumulating in the nocturnal boundary layer when vertical mixing is weak. We observed significant seasonal trends in Δ14C-CO2 at different soil depths that reflected changes in the shares of autotrophic and heterotrophic respiration. Also the observed diurnal variation in the Δ14C values in soil CO2 highlighted the changes in the origin of CO2, with root activity decreasing more for the night than decomposition.
Energy Flow and Food Web Ecology along a Hydroperiod Gradient

Identifying the ecological mechanisms that determine food web structure is critical for understanding the causes and consequences of diversity. The objective of this thesis was to identify the mechanisms structuring aquatic food webs across environmental gradients from a multi-level perspective (individual to ecosystem) using integrative methodology and field experiments to test classic ecological theory. My results demonstrate support for the dynamic constraints hypothesis, which predicts habitats with greater disturbance should have shorter food chains, but are not consistent with the ecosystem size hypothesis that predicts larger ecosystems have longer food chains. Insect and amphibian richness increased with increasing pond size and hydroperiod, indicating that insertion of new consumers into pond communities was driving variation in food-chain length. A multivariate analysis testing the influence of physicochemical variables on food-web characteristics revealed that hydroperiod and pond area had a strong influence on amphibian and invertebrate assemblages, trophic diversity and  15 N range. Foodchain length did not respond strongly to any one variable, but instead responded weakly to multiple environmental variables, suggesting interacting influences on food-web structure. Conversely, the trophic niche of amphibian larvae was not influenced by pond hydroperiod, but did exhibit ontogenetic diet shifts. Populations of amphibian larvae with broader niche widths iii also had increased individual variation, supporting the niche variation hypothesis. In addition, I assessed whether species diversity influenced the magnitude of cross-habitat resource flow between aquatic and terrestrial habitats via emerging aquatic insects, metamorphosing amphibians, and litter deposition. Deposition into ponds far exceeded carbon exported via insect and amphibian emergences. We found a negative relationship between resource flux and the diversity of amphibians and insects, which contradicts the general pattern of positive biodiversity-ecosystem function relationships. My research strongly suggests environmental variation is a key process in shaping food-web structure and function and that multiple methodologies are needed to understand temporal and spatial dynamics of aquatic ecosystems.
Urea and chronic kidney disease: the comeback of the century? (in uraemia research)

Urea, a marker of uraemic retention in chronic kidney disease (CKD) and of adequacy of intradialytic solute removal, has traditionally been considered to be biologically inert. However, a number of recent experimental data suggest that urea is toxic at concentrations representative for CKD. First of all, at least five studies indicate that urea itself induces molecular changes related to insulin resistance, free radical production, apoptosis and disruption of the protective intestinal barrier. Second, urea is at the origin of the generation of cyanate, ammonia and carbamylated compounds, which as such all have been linked to biological changes. Especially carbamylation has been held responsible for post-translational protein modifications that are involved in atherogenesis and other functional changes. In observational clinical studies, these carbamylated compounds were associated with cardiovascular and overall morbidity and mortality. These findings shed new light on the validity of Kt/Vurea as a marker of dialysis adequacy. Yet, also the views that the kinetics of urea are not representative of the kinetics of several other uraemic retention solutes, and that urea cannot be held responsible for all complex metabolic and clinical changes responsible for the uraemic syndrome, still remain valid. Future efforts to improve the outcome of patients with CKD might be directed at further improving removal of solutes implied in the uraemic syndrome, including but not restricted to urea, also taking into account the impact of the intestine and (residual) renal function on solute concentration.