Miracle-dz/UniFAR-FTUs huggingface dataset:
Methamphetamine-related emergency department utilization and cost.

OBJECTIVE To quantify the frequency, cost, and characteristics associated with emergency department (ED) visits that are related to methamphetamine use. METHODS This was a prospective observational study. The authors performed a training program for ED clinicians on the acute and chronic effects of methamphetamine and the signs of methamphetamine abuse. A standardized two question survey was administered to clinicians concerning the relationship between the ED visit and the patient's methamphetamine use. The survey was embedded in the patient tracking system and was required for all ED patients before disposition. Survey results were merged with administrative data on demographics, diagnosis, disposition, and charges. Univariate analyses were used to determine patient characteristics associated with methamphetamine-related ED visits. RESULTS The authors examined 15,038 ED visits over a 20-week period from February 2006 to June 2006. There were a total of 353 methamphetamine-related visits, for an average of 17.65 visits per week (2.4% of all visits). Hospital charges for methamphetamine-related ED visits averaged $133,181 per week, for an estimated total of $6.9 M in annual charges. Methamphetamine-related ED patients were more likely to be male (odds ratio [OR] 1.6, 95% confidence interval [CI] = 1.30 to 2.01), white (OR 1.8, 95% CI = 1.38 to 2.29), and uninsured (OR 3.2, 95% CI = 2.21 to 4.69). The top four medical conditions associated with methamphetamine-related visits were mental health (18.7%), trauma (18.4%), skin infections (11.1%), and dental diagnoses (9.6%). CONCLUSIONS Methamphetamine abuse accounts for a modest but substantial proportion of ED utilization and hospital cost. Methamphetamine-related ED visits are most commonly related to mental illness, trauma, skin, and dental-related problems.
Sp1 phosphorylation by ATM downregulates BER and promotes cell elimination in response to persistent DNA damage

Abstract ATM (ataxia-telangiectasia mutated) is a central molecule for DNA quality control. Its activation by DNA damage promotes cell-cycle delay, which facilitates DNA repair prior to replication. On the other hand, persistent DNA damage has been implicated in ATM-dependent cell death via apoptosis; however, the mechanisms underlying this process remain elusive. Here we find that, in response to persistent DNA strand breaks, ATM phosphorylates transcription factor Sp1 and initiates its degradation. We show that Sp1 controls expression of the key base excision repair gene XRCC1, essential for DNA strand break repair. Therefore, degradation of Sp1 leads to a vicious cycle that involves suppression of DNA repair and further aggravation of the load of DNA damage. This activates transcription of pro-apoptotic genes and renders cells susceptible to elimination via both apoptosis and natural killer cells. These findings constitute a previously unrecognized ‘gatekeeper’ function of ATM as a detector of cells with persistent DNA damage.
Prevalence of Occult Celiac Disease in Patients with Iron-Deficiency Anemia: A Prospective Study

Background Occult celiac disease has been reported in 0 to 6% of adults presenting with iron-deficiency anemia. Most prior studies have been retrospective or screened only a selected population of patients with small bowel biopsies. To more accurately define the true prevalence of this disorder in patients presenting with iron-deficiency anemia (with or without stool hemoccult positivity), we initiated this prospective study. Methods Esophagogastroduodenoscopy with small bowel biopsies and colonoscopy were performed in all iron-deficiency anemia patients (including those with hemoccult-positive stools) referred to the gastroenterology service during a 2-year period (1998–2000). Inclusion criteria included iron-deficiency anemia as defined by a serum ferritin <25 ng/ml and anemia with hemoglobin <12 g/dl. Patients were excluded for documented prior erosive, ulcerative, or malignant disease of the gastrointestinal tract, previous gastrointestinal surgery, overt gastrointestinal bleeding within the past 3 months, or inability to access the duodenum for biopsy. All patients underwent upper endoscopy with more than two biopsies of the distal duodenum and colonoscopy. A serum immunoglobulin A antiendomysial antibody test was to be performed in those patients with a positive small bowel biopsy to confirm the diagnosis of celiac disease. Results One hundred five of 139 consecutive patients with iron-deficiency anemia met the inclusion criteria and were enrolled in the study. Fifty-seven men (mean age, 51.6 yr) and 48 women (mean age, 54.1 yr) constituted the study population. The demographics of this study population included 36 blacks, 38 Hispanics, and 22 whites. Nine patients were of mixed or unknown ethnic background. Forty-three and eight-tenths percent of the men and 37.5% of women had hemoccult-positive stools, accounting for a total of 40.9% of the study patients. Upper endoscopic findings included gastritis in 22.8%, gastric ulcers in 9.5%, duodenitis in 8.5%, esophagitis in 7.6%, Barrett’s ulcer in 2.8%, duodenal ulcer in 2.8%, gastric polyp in 2.8%, and celiac disease in 2.8%. Colonoscopic findings included colon polyps in 21.9%, diverticula in 10.4%, and hemorrhoids in 16.1%. Multiple findings were found in 32.3% of patients, and there were no findings in 28.5% of patients. Conclusion The prevalence of occult celiac disease in this prospective study of patients presenting with iron-deficiency anemia was 2.8%. A significant number of other gastrointestinal lesions amenable to therapy were also found on upper and lower endoscopy in these patients. Given the treatable nature of celiac disease, it should be screened for in patients with unexplained iron-deficiency anemia with or without hemoccult-positive stools.
Marine Ecology Progress Series Mar Ecol Prog Ser Protective Capacity of Mangroves during Tropical Storms: a Case Study from 'wilma' and 'gamma' in Belize

Globally threatened mangrove forest habitat is often considered an important buffer protecting coastlines from wave and storm impacts and coastal erosion. However, there is little empirical data quantifying the protective effects of mangroves during storms, primarily because of the difficulty of predicting where and when a storm will intersect the shoreline, to facilitate data collection before and after storm events. In 2005, opportunistic results from an ongoing study quanti­ fying differences between intact and cleared mangrove areas on Turneffe Atoll, Belize, provided such pre-and post-storm data from tropical storms 'Wilma' (later a Category 5 Hurricane) and 'Gamma'. We compared differences in equipment retention rates of 3 types of experimental devices previously installed in adjacent intact and cleared mangrove areas. Retention rates were greater in intact mangrove areas, empirically demonstrating the protective capacity of mangroves during moderate magnitude storm events. The results support the assumption that removal of mangroves diminishes coastal protection not only during catastrophic storm events such as hurricanes or tsunamis, but also during less energetic but more frequent events, such as tropical storms. This high­ lights the importance of improved coastal zone management, as storm events may increase in frequency and intensity with changing climate, and coastal mangrove forest habitats continue to decline in size and number. Resale or republication not permitted without written consent of the publisher
Tumor Microenvironment Landscapes Supporting EGFR-mutant NSCLC Are Modulated at the Single-cell Interaction Level by Unesbulin Treatment

Abstract Lung cancer is the leading cause of cancer deaths. Lethal pulmonary adenocarcinomas (ADC) present with frequent mutations in the EGFR. Genetically engineered murine models of lung cancer expedited comprehension of the molecular mechanisms driving tumorigenesis and drug response. Here, we systematically analyzed the evolution of tumor heterogeneity in the context of dynamic interactions occurring with the intermingled tumor microenvironment (TME) by high-resolution transcriptomics. Our effort identified vulnerable tumor-specific epithelial cells, as well as their cross-talk with niche components (endothelial cells, fibroblasts, and tumor-infiltrating immune cells), whose symbiotic interface shapes tumor aggressiveness and is almost completely abolished by treatment with Unesbulin, a tubulin binding agent that reduces B cell–specific Moloney murine leukemia virus integration site 1 (BMI-1) activity. Simultaneous magnetic resonance imaging (MRI) analysis demonstrated decreased tumor growth, setting the stage for future investigations into the potential of novel therapeutic strategies for EGFR-mutant ADCs. Significance: Targeting the TME is an attractive strategy for treatment of solid tumors. Here we revealed how EGFR-mutant landscapes are affected at the single-cell resolution level during Unesbulin treatment. This novel drug, by targeting cancer cells and their interactions with crucial TME components, could be envisioned for future therapeutic advancements.
A multicomponent coupled model of glacier hydrology 2. Application to Trapridge Glacier, Yukon, Canada

[1] A new glaciohydraulic model is tailored to Trapridge Glacier, Yukon, Canada, where long-term measurements of subglacial water pressure provide parameter constraints and a platform for model evaluation. Using digital elevation models and meteorological data as input, we investigate hydrology on diurnal and seasonal timescales. Quantitative comparisons of simulated and observed pressure records allow us to select a reference model objectively, from which we gain first insights into the gross spatial characteristics of the drainage system. Equilibrium simulations highlight target areas for water storage and potential sticky spots, both of which have established relevance to glacier dynamics. Seasonal simulations capture the key signatures of spring and autumn transitions and corroborate our understanding of the processes involved. Successfully modeled features of the spring transition include increased hydraulic coupling between the surface and bed with time, temporary augmentation of subglacial storage, and rapid subglacial transitions from a hydraulically unconnected to connected state. Autumn transitions are characterized by deterioration of the basal drainage network, drawdown of subglacial storage reservoirs, and heightened sensitivity to precipitation and surface refreezing. Finally, we draw attention to the important role of groundwater transport in cold glacial environments where permafrost can impede drainage from the ice margin.
Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.
Paleoaltimetry Potentiality of Branched GDGTs From Southern Tibet

Paleoaltimetric reconstructions of the southern Tibetan Plateau (TP) are crucial to understand the processes and mechanisms concomitant with the tectonic collision of the Indian and Eurasian continental plates. We measured the branched glycerol dialkyl glycerol tetraether (brGDGT) indices from 88 surface soils from the southern TP and found that alkaline soils exhibited lower MBT′ and MBT′/CBT‐derived MAT (mean annual temperature), while MBT′/CBT‐derived MAT exhibited a strong correlation with altitude (R2 = 0.84; n = 63) for all of the localities with neutral and acidic soils. Differently, we found that MBT′5ME‐derived MAT exhibited a strong relation with altitude even though a mixture of alkaline samples (R2 = 0.72; n = 83). As a result, two regional calibrations were developed, including a neutral and acidic soil calibration based on MBT′/CBT‐MAT and a calibration suitable for both acidic and alkaline soils based on MBT′5ME‐MAT for the southern TP. Based on this new soil calibration data set, and a recent global soil calibration data set founded on MBT′5ME, we calculated paleo‐MAT of ∼9.49 ± 1.15 to 10.38 ± 1.47°C at ∼15 Ma, respectively, for the Namling Basin. Applying these soil calibrations, the paleoaltitudes of the Namling Basin can be calculated to have been between 4.36 ± 0.41 km above sea level (asl) and 4.43 ± 0.36 km asl at ∼15 Ma, respectively, similar to the paleoaltitudes of ∼4.7–5.4 km asl at ∼15 Ma inferred from the floral physiognomy of Namling Basin fossils and stable isotopes. These findings would suggest the applicability of MBT′/CBT (and/or MBT′5ME) indices as paleotopographic and paleotemperature proxies on the southern TP.
The Effect of Information Technology-Enabled Flexibility on Formation and Market Value of Alliances

This study investigates the effect of information technology IT architecture flexibility on strategic alliance formation and firm value. We first examine the effect of three dimensions of IT architecture flexibility open communication standards, cross-functional transparency, and modularity on formation of three types of alliances arm's-length, collaborative, and joint-venture alliances, respectively. Then, we examine how capabilities in IT flexibility can enhance the value derived from alliances. Our sample includes data from 169 firms that are publicly listed in the United States and that span multiple industries. We find that adoption of open communication standards is associated with the formation of arm's-length alliances, and modularity of IT architecture is associated with the formation of joint ventures. We also find that IT architecture flexibility enhances the value of arm's-length, collaborative, and joint-venture alliances. The contribution of IT flexibility to value is greater in the case of collaborative alliances than in arm's-length alliances. Taken together, these findings suggest that appropriate investments in IT can help to facilitate reconfiguration of resources and modification of processes in collaboration-intensive alliances. This paper was accepted by Ramayya Krishnan, information systems.
Applications of intuitionistic logic in Answer Set Programming

We present some applications of intermediate logics in the field of Answer Set Programming (ASP). A brief, but comprehensive introduction to the answer set semantics, intuitionistic and other intermediate logics is given. Some equivalence notions and their applications are discussed. Some results on intermediate logics are shown, and applied later to prove properties of answer sets. A characterization of answer sets for logic programs with nested expressions is provided in terms of intuitionistic provability, generalizing a recent result given by Pearce. It is known that the answer set semantics for logic programs with nested expressions may select non-minimal models. Minimal models can be very important in some applications, therefore we studied them; in particular we obtain a characterization, in terms of intuitionistic logic, of answer sets which are also minimal models. We show that the logic G3 characterizes the notion of strong equivalence between programs under the semantic induced by these models. Finally we discuss possible applications and consequences of our results. They clearly state interesting links between ASP and intermediate logics, which might bring research in these two areas together.
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides

Abstract ‘Superbugs’ have received increasing attention from researchers, such as ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.), which directly led to about 1 270 000 death cases in 2019. Recently, phage peptidoglycan hydrolases (PGHs)–derived antimicrobial peptides were proposed as new antibacterial agents against multidrug-resistant bacteria. However, there is still a lack of methods for mining antimicrobial peptides based on phages or phage PGHs. Here, by using a collection of 6809 genomes of ESKAPE isolates and corresponding phages in public databases, based on a unified annotation process of all the genomes, PGHs were systematically identified, from which peptides were mined. As a result, a total of 12 067 248 peptides with high antibacterial activities were respectively determined. A user-friendly tool was developed to predict the phage PGHs–derived antimicrobial peptides from customized genomes, which also allows the calculation of peptide phylogeny, physicochemical properties, and secondary structure. Finally, a user-friendly and intuitive database, ESKtides (http://www.phageonehealth.cn:9000/ESKtides), was designed for data browsing, searching and downloading, which provides a rich peptide library based on ESKAPE prophages and phages. Database URL: 10.1093/database/baae022
Serum concentration effects on the kinetics and metabolism of hela-s3 cell growth and cell adaptability for successful proliferation in serum free medium

The effect of serum content of culture medium on the kinetics of cell growth and metabolism has been studied in HeLa S3 culture. Increasing the serum concentration from 5 to 15% in Ham's F12 mediu m increased the total number of living cells by about 30%. Further increase in serum concentration resulted in significant reduction in viable cell number. Meanwhile, increasing serum concentration in culture medium from 5 to 20% shows positive effect on cell viability and increased it from 38 to 74% in 144 h cultivated cultures. On the other hand, both of glucose consumption and lactate production rates were increased by the increase of serum concentration in the range between 5 and 20%. Based on these data, cells grown in Ham's F12 medium of 10% serum were used for adaptation to serum free medium (SFM). Successive adaptation of cells to complete SFM was done by cultivating cells in different passages with the increased fraction of SFM in the cultivation medium. The ratios between SM (Ham's F12 supplemented with 10%) to SFM (SMIF-6) were (100:0; 75:25; 50:50; 25:75; 10:90; 0:100). For each medium, cells were cultivated in 2-3 short passages for only 72 h to keep the cells in all cultures in their mid-exponential phase. Based on this cultivation strategy, HeLa S3 cells were completely adapted to serum free medium in only 880 hours. Neither growth kinetics nor physiological characterization (based on the data of glucose consumption rate and lactate production rate) were changed during the cell adaptation to SFM.
DOES GRIEF COUNSELING WORK?

Most bereavement caregivers accept as a truism that their interventions are helpful. However, an examination of the bereavement intervention literature suggests that the scientific basis for accepting the efficacy of grief counseling may be quite weak. This article summarizes the findings of four recent qualitative and quantitative reviews of the bereavement intervention literature. It then discusses three possible explanations for these surprising findings and concludes with recommendations for both researchers and clinicians in thanatology that could help to focus efforts to answer the questions of when and for whom grief counseling is helpful.
Protease Inhibitor Resistance Analysis in the MONARK Trial Comparing First-Line Lopinavir-Ritonavir Monotherapy to Lopinavir-Ritonavir plus Zidovudine and Lamivudine Triple Therapy

ABSTRACT The MONARK study was a pilot randomized trial comparing the safety and efficacy of lopinavir-ritonavir (LPV/r) monotherapy to those of LPV/r-zidovudine-lamivudine triple therapy for antiretroviral-naïve human immunodeficiency virus type 1 (HIV-1)-infected patients. Resistance testing was performed at the time of initial screening and at the time of virological failure (defined to include low-level viremia with >50 and <400 HIV-1 virus RNA copies/ml of plasma). Changes from the baseline sequences, including mutations noted on the 2008 International AIDS Society—USA list of resistance-associated protease mutations, were considered. Drug resistance testing was performed for 38 patients (5 of 53 on triple therapy and 33 of 83 on monotherapy). By week 96 (W96), virus samples from 18 of 33 patients in the monotherapy arm showed changes from baseline sequences, and 5 of these patients had viruses with major protease inhibitor (PI) resistance-associated mutations (M46I at W40, L76V at W48, M46I and L76V at W48, L10F and V82A at W72, and L76V at W84). Data on virus phenotypes detected at the time of initial screening and the time of virological failure were available for four patients in whom major PI resistance mutations developed, and these data revealed a mean increase of 2.2-fold (range, 0.75- to 4.6-fold) in the LPV 50% inhibitory concentration. All three patients in whom the L76V PI resistance mutation developed were infected with HIV-1 subtype CRF02_AG. In the triple-therapy group, no major PI resistance mutation was selected among the three patients with protease changes by W48. No association between the baseline CD4 cell count and the viral load, the W4 and final viral loads, or the final LPV trough concentration and the emergence of a major PI resistance mutation was found. Major PI resistance-associated mutations were detected in 5 (6%) of 83 patients treated with LPV/r monotherapy, suggesting that LPV/r monotherapy is an inappropriate first option. The mutation L76V may be considered in further studies of lopinavir resistance.
Promoting the use of end-to-end congestion control in the Internet

This paper considers the potentially negative impacts of an increasing deployment of non-congestion-controlled best-effort traffic on the Internet. These negative impacts range from extreme unfairness against competing TCP traffic to the potential for congestion collapse. To promote the inclusion of end-to-end congestion control in the design of future protocols using best-effort traffic, we argue that router mechanisms are needed to identify and restrict the bandwidth of selected high-bandwidth best-effort flows in times of congestion. The paper discusses several general approaches for identifying those flows suitable for bandwidth regulation. These approaches are to identify a high-bandwidth flow in times of congestion as unresponsive, "not TCP-friendly", or simply using disproportionate bandwidth. A flow that is not "TCP-friendly" is one whose long-term arrival rate exceeds that of any conformant TCP in the same circumstances. An unresponsive flow is one failing to reduce its offered load at a router in response to an increased packet drop rate, and a disproportionate-bandwidth flow is one that uses considerably more bandwidth than other flows in a time of congestion.