Miracle-dz/UniFAR-FTUs huggingface dataset:
MYELOID NEOPLASIA Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML

There is interest in using leukemia-gene panels and next-generation sequencing to assess acute myelogenous leukemia (AML) response to induction chemotherapy. Studies have shown that patients with AML in morphologic remission may continue to have clonal hematopoiesis with populations closely related to the founding AML clone and that this confers an increased risk of relapse. However, it remains unknown how induction chemotherapy influences the clonal evolution of a patient’s nonleukemic hematopoietic population. Here, we report that 5 of 15 patients with genetic clearance of theirfoundingAMLcloneafterinductionchemotherapyhadaconcomitantexpansionofa hematopoieticpopulationunrelatedtotheinitialAML.Thesepopulationsfrequentlyharboredsomaticmutationsingenesrecurrently mutated in AML or myelodysplastic syndromes and were detectable at very low frequencies at the time of AML diagnosis. These resultssuggestthatnonleukemichematopoietic stemandprogenitor cells,harboringspecificaging-acquiredmutations, mayhavea competitive fitness advantage after induction chemotherapy, expand, and persist long after the completion of chemotherapy. Although the clinical importance of these “rising” clones remains to be determined, it will be important to distinguish them from leukemia-related populations when assessing for molecular responses to induction chemotherapy. ( Blood . 2016;127(7):893-897)
Static load test interpretation using the t-z model and LRFD resistance factors for auger cast-in-place (AC IP) and drilled displacement (DD) piles

Abstract Static load test data for augered cast-in-place (ACIP) and drilled displacement (DD) piles were interpreted using the t-z model method. Eighteen load tests consisting of load-settlement and load transfer data were obtained from two different construction sites. A series of back-calculations were performed using the t-z model method to enhance the static load test data, which were then analyzed to obtain resistance bias factors for the currently used ACIP and DD pile design methods. The t-z model method enhanced load test data provides the ability to interpret field data for loading conditions beyond those measured during test. The resistance bias for the various design methods were then used to obtain the resistance factors based upon the traditional calibration approach. Furthermore, resistance factors were also obtained using probabilistic analysis based upon the t-z model method. The comparison of these two sets of resistance factor indicates that those obtained from the traditional calibration approach contain a wide range of magnitudes, while the resistance factors from the t-z model method design result in a consistent level of reliability.
Plants cultivated for ecosystem restoration can evolve toward a domestication syndrome

Significance Globally upscaling demands for native seeds for ecosystem restoration can be covered by agricultural seed propagation. Yet, agricultural practice can unintentionally select for specific traits and reduce adaptive variability, which could affect plant performance once sown back to the wild. We show, across 19 wild species, two seed producers and up to four consecutive cultivated generations, that some plants under cultivation evolved higher vigor, reduced adaptive variability, synchronized flowering and in one case, reduced seed shattering. Yet, there were substantial differences among cultivation lineages, with negligible changes in most, and large changes only in a few cases. Substantial unintended evolution in cultivation is thus rather an exception than the rule.
Reach Sensitivity Index Mapping of the Amite River Watershed in the Lake Pontchartrain Basin: A Tool for Watershed Restoration

Abstract In recent years, the focus on issues regarding water quality has shifted from a local site-specific view of a problem toward a holistic view where the health and hydrologic functionality of entire watersheds are of concern. One measure of watershed health is fluvial geomorphology. The goal of this project was to map the morphology of the streams of the Amite watershed of the Pontchartrain Basin using a reach sensitivity index (RSI). The classification scale is based on stream geomorphology, hydrology, and ecological characteristics, where rank is given based on morphological complexity and associated wetlands. The RSI classification method used data from 18 field sites along with digital orthophoto quarter quadrangle 1-m resolution infrared aerial imagery, gap analysis program land cover data, and digital elevation models generated from light detection and ranging. In addition to mapping, issues related to watershed impairment and restoration were identified. Key anthropogenic impacts observed include sand and gravel mining, stream manipulation, profuse litter, and overall water quality. The watershed in this study is proximal to urban areas associated with New Orleans and Baton Rouge, Louisiana, so another theme, waterfront development, was also identified as a source of stream impairment. Reach sensitivity index stream classification can serve as a tool for conservation strategies and watershed restoration, where the ultimate goal is to restore natural hydrological and ecological functionality to impaired streams. Maps generated in the RSI project can further aid in regional planning, without which, rapid urban development and continued stream manipulation within the Amite and neighboring stream systems will result in accelerated watershed impairment and water-quality degradation.
EXPLORING THE RELATIONSHIP BETWEEN SPIRITUAL WELL-BEING AND SMOKING CESSATION TREATMENT

ABSTRACT UNDERSTANDING THE ROLE OF SPIRITUAL WELL-BEING IN A SMOKING CESSATION PROGRAM Kia Kerrin, MSW Ram Cnaan, Ph.D. Tobacco use, particularly cigarette smoking, is the single most preventable cause of death in the United States of America. The negative health effects of cigarette smoking are a major public health concern that can be reduced through quitting. Preliminary data has shown that spirituality can aid in the success of addiction treatment programs and smoking cessation programs. However, the current data are limited in their support of the relationship between spirituality and smoking cessation. This research study further explored the relationship between spiritual well-being and smoking cessation. A sample of 178 cigarette smokers was included in the research study to assess the relationship between levels of spiritual well-being and abstinence after an 8 week nicotine patch smoking cessation treatment program. The study was conducted through the University of Pennsylvania and Northwestern University. The proposed study was completed in conjunction with an ongoing NIH-funded clinical trial (R01 DA025078; An Effectiveness Trial of Maintenance Therapy for Nicotine Dependence). The proposed study involved the inclusion of a spiritual well-being scale at the baseline session. Subjects received the 21mg transdermal nicotine patch for 8 weeks, along with smoking cessation counseling. The Spiritual Well Being scale was utilized to determine if spiritual well-being was a predictor of abstinence at the 8 week mark. This research study was intended to be a catalyst to determine whether spirituality should play a part in smoking cessation programs. Concerning the relationship between the spiritual well-being scale and quitting smoking and the spiritual well-being scale and dropping out of the smoking cessation program, there were no significant findings. Although, these main relationships were not found there were other significant relationships that may suggest these areas should be explored in more depth. Relationships were found between religious well-being and compliance with patch usage. The initial findings also suggest there is a relationship between scores of religious well being and race. Degree Type Dissertation Degree Name Doctor of Social Work (DSW) First Advisor Ram Cnaan, PhD This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations_sp2/70 Second Advisor Robert Schnoll, PhD Third Advisor E. Paul, Wileyto, PhD
Quantitative profiling of the endonuclear glycerophospholipidome of murine embryonic fibroblasts

A reliable method for purifying envelope-stripped nuclei from immortalized murine embryonic fibroblasts (iMEFs) was established. Quantitative profiling of the glyc-erophospholipids (GPLs) in envelope-free iMEF nuclei yields several conclusions. First, we find the endonuclear glycerophospholipidome differs from that of bulk membranes, and phosphatidylcholine
Injection of iodine to the stratosphere

We report a new estimation of the injection of iodine into the stratosphere based on novel daytime (solar zenith angle < 45°) aircraft observations in the tropical tropopause layer and a global atmospheric model with the most recent knowledge about iodine photochemistry. The results indicate that significant levels of total reactive iodine (0.25–0.7 parts per trillion by volume), between 2 and 5 times larger than the accepted upper limits, can be injected into the stratosphere via tropical convective outflow. At these iodine levels, modeled iodine catalytic cycles account for up to 30% of the contemporary ozone loss in the tropical lower stratosphere and can exert a stratospheric ozone depletion potential equivalent to, or even larger than, that of very short‐lived bromocarbons. Therefore, we suggest that iodine sources and chemistry need to be considered in assessments of the historical and future evolution of the stratospheric ozone layer.
Causes and impacts of the 2014 warm anomaly in the NE Pacific

Strongly positive temperature anomalies developed in the NE Pacific Ocean during the boreal winter of 2013–2014. Based on a mixed layer temperature budget, these anomalies were caused by lower than normal rates of the loss of heat from the ocean to the atmosphere and of relatively weak cold advection in the upper ocean. Both of these mechanisms can be attributed to an unusually strong and persistent weather pattern featuring much higher than normal sea level pressure over the waters of interest. This anomaly was the greatest observed in this region since at least the 1980s. The region of warm sea surface temperature anomalies subsequently expanded and reached coastal waters in spring and summer 2014. Impacts on fisheries and regional weather are discussed. It is found that sea surface temperature anomalies in this region affect air temperatures downwind in Washington state.
Air‐sea interactions over Terra Nova Bay during winter: Simulation with a coupled atmosphere‐polynya model

A preliminary simulation of the Terra Nova Bay polynya has been performed with a coupled atmosphere-polynya model. The atmospheric model is a hydrostatic primitive equations model that has been validated previously by a simulation of the strong katabatic winds observed in that area. The polynya model includes a representation of the free drift of frazil ice and simple sea-ice dynamics and thermodynamics. Two and three-dimensional experiments have been performed under polar night conditions. Two-dimensional experiments show that an open (warm) water area influences significantly the atmospheric circulation in the antarctic coastal zone: an additional ice-breeze effect is simulated and is responsible for the strenghthening of the katabatic winds near the coast. Because of the important temperature difference between the continental air and the ice-free ocean (up to 40°C), strong surface heat fluxes are simulated over the polynya. Finally, a three-dimensional experiment has been performed. The integration domain includes Terra Nova Bay. The polynya observed in that region is well simulated. It is found that heat losses from the polynya surface are stronger than previously thought but are probably constrained by the idealized representation of frazil ice, which is assumed to be uniform in each grid box. This stresses the need for having a better knowledge of frazil ice evolution in large polynyas.
The rate of adaptive molecular evolution in 1 wild and domesticated Saccharomyces 2 cerevisiae populations 3

16 Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of 17 civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology 18 giving rise to bona fide domesticated lineages. Here, we conduct a population genomic study of both 19 domesticated and wild lineages of S. cerevisiae . Using coalescent analyses, we report that the effective 20 population size of yeast populations decreased since the divergence with S. paradoxus . We fitted models 21 of distribution of fitness effects to population genomic data sets to infer the rate of adaptive non- 22 synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive 23 selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared 24 to domesticated populations. We find that populations with a larger effective population size experience a 25 lower rate of non-adaptive substitutions, as well as a higher rate of adaptive ones, suggesting that, in yeast, 26 adaptive mutations accumulate at a faster rate in large populations. Our analyses revealed the signature of 27 background selection but no Hill-Robertson interference, as recombination was found to mildly impact the 28 efficacy of purifying selection and does not affect the rate of adaptive evolution in yeast. Conversely, the 29 rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, 30 a relation that cannot be explained by the population’s demography. Together, our results provide a detailed 31 characterization of adaptive mutations across S. cerevisiae genomes and populations. 32
Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box motifs

The mammalian circadian clock is based on a core intracellular gene regulatory network, coordinated by communication between the central nervous system and peripheral tissues like the liver. Transcriptional and translational feedback loops underlie the molecular mechanism of circadian oscillation and generate its 24 h periodicity. The Brain and muscle Arnt-like protein-1 (Bmal1) forms a heterodimer with Circadian Locomotor Output Cycles Kaput (Clock) that binds to E-box gene regulatory elements, activating transcription of clock genes. In this work we aimed to develop a predictive model of genome-wide CLOCK-BMAL1 binding to E-box motifs. We found over-representation of the canonical E-box motif CACGTG in BMAL1-bound regions in accessible chromatin of the mouse liver, heart and kidney. We developed three different tissue-specific machine learning models based on DNA sequence, DNA sequence plus DNA shape, and DNA sequence and shape plus histone modifications. Combining DNA sequence with DNA shape and histone modification features yielded improved transcription factor binding site prediction. Further, we identified the genomic and epigenomic features that best correlate to the binding of BMAL1 to DNA. The DNA shape features Electrostatic Potential, Minor Groove Width and Propeller Twist together with the histone modifications H3K27ac, H3K4me1, H3K36me3, and H3K4me3 were the features most highly predictive of DNA binding by BMAL1 across all three tissues.
Drug therapy in patients with chronic renal failure.

BACKGROUND Roughly 20% of patients in hospital have impaired kidney function. This is frequently overlooked because of the creatinine-blind range in which early stages of renal failure are often hidden. Chronic kidney disease is divided into 5 stages (CKD 1 to 5). METHODS Selective literature search. RESULTS Methotrexate, enoxaparin and metformin are examples of drugs that should no longer be prescribed if the glomerular filtration rate (GFR) is 60 mL/min or less. With antidiabetic (e.g. glibenclamide), cardiovascular (e.g. atenolol) or anticonvulsive (e.g. gabapentin) drugs, the advice is to use alternative preparations such as gliquidone, metoprolol or carbamazepine which are independent of kidney function. Drug dose adjustment should be considered with antimicrobial (e.g. ampicillin, cefazolin), antiviral (e.g. aciclovir, oseltamivir) and, most recently, also for half of all chemotherapeutic and cytotoxic drugs in patients with impaired kidney function (with e.g. cisplatin, for instance, but not with paclitaxel). CONCLUSION Decisions concerning drug dose adjustment must be based on the pharmacokinetics but this is an adequate prerequisite only in conjunction with the pharmacodynamics. There are two different dose adjustment rules: proportional dose reduction according to Luzius Dettli, and the half dosage rule according to Calvin Kunin. The latter leads to higher trough concentrations but is probably more efficient for anti-infective therapy.
Growing up in a domestic violence environment: relationship with developmental trajectories of body mass index during adolescence into young adulthood

Background This study investigated the relationship between growing up in a violent home and developmental trajectories of body mass index (BMI) in a cohort of adolescents followed longitudinally from 1996 to 2003 e 4. Methods 6043 girls and 4934 boys aged 9 e 14 years in 1996 who reported height and weight at least two times and whose mothers completed intimate partner violence (IPV) questions at the 2001 Nurses’ Health Study. Main exposure was experiencing the ﬁrst family violence during early (0 e 5 years) or later (6 e 11 years) childhood, based on mother’s year-speciﬁc exposure of IPV and the birth year of each participant. Mother’s report of IPV was ascertained by the abuse assessment screen. Four distinct BMI trajectory groups were estimated from age-speciﬁc BMI (age 12 e 20 years), using general growth mixture modelling. Results Four distinct BMI trajectories were identiﬁed separately for girls and boys: healthy growth; healthy to obese; steady overweight and consistently obese. Compared with boys not exposed to violence at home, boys raised in violent homes before 5 years were at increased risk of being in the consistently obese (OR ¼ 2.0; 95% CI 1.2 to 3.5) and steady overweight (OR 1.4; 95% CI 1.1 to 1.9) groups after adjusting for confounders. Girls raised in violent homes were more likely to be in the steady overweight group, but associations did not maintain statistical signiﬁcance after adjusting for confounding. Conclusion link children’s exposure to domestic violence to a risk of unhealthy weight trajectories during adolescence in boys. Detrimental effects of exposure to a domestic violence environment may take root in the ﬁrst few years of development for boys.
Macrophages Are More Potent Immune Suppressors Ex Vivo Than Immature Myeloid-Derived Suppressor Cells Induced by Metastatic Murine Mammary Carcinomas

Myeloid-derived suppressor cells (MDSCs) are emerging as potential promoters of metastatic tumor growth, and there is interest in targeting immature MDSCs by inducing their differentiation into more mature myeloid cells. We used all-trans retinoic acid (ATRA) to differentiate MDSCs in mice bearing metastatic 4T1 or 4TO7 murine mammary tumors, and assessed the immune-suppressive mechanisms and potencies of different myeloid cell subpopulations. Metastatic mammary tumors induced the accumulation of distinct populations of immature CD11b+Gr1+F4/80−Ly6CmidLy6G+ MDSCs (“Gr1+ cells”) and mature CD11b+Gr1−F4/80+ cells (“F4/80+ cells”) in metastatic target organs. ATRA triggered the differentiation of Gr1+ cells into F4/80+ cells in the lungs and, unexpectedly, enhanced pulmonary metastatic tumor growth. We found that F4/80+Ly6C−Ly6G− mature macrophages (Mϕs) were up to 30-fold more potent immune suppressors than Gr1+ cells on a per-cell basis, which we postulate may contribute to the increased metastatic growth observed with ATRA treatment. F4/80+ cells and Gr1+ cells used different reactive oxygen species (ROS)–mediated mechanisms of immunosuppression ex vivo, with F4/80+ cells producing higher levels of ROS, which is consistent with their superior immunosuppressive abilities. These data highlight the potent immunosuppressive functions of Mϕs, reveal that Mϕs can suppress T cell responses via ROS production, and suggest that ROS inhibitors may be useful in promoting antitumor immune responses. Our findings also caution against using ATRA to modulate myeloid cell differentiation and function to treat breast cancer metastases in the lung, and support the development of therapeutic strategies to enhance antitumor immunity by targeting myeloid cells as a collective group.
Learning Minimally Invasive Mitral Valve Surgery : A Cumulative Sum Sequential Probability Analysis of 3895 Operations From a Single

Nonaortic cardiac surgery is associated with a low but significant incidence of type A aortic dissection (AAD). Because there are important differences in clinical presentation, surgical management, and prognosis between spontaneous and late AAD following cardiac surgery, this large multicenter study sought to determine the conditions associated with the high surgical mortality of AAD repair as a complication of nonaortic cardiac surgery and to identify management pathways to improve outcome. We found that operative mortality depends on the type of initial surgery, time to AAD, and, importantly, influenceable management factors. AAD occurred mainly in patients with preexisting aortic wall pathology, identifiable with a slightly enlarged aorta, and hypertension at sites of iatrogenic mechanical trauma. This finding emphasizes most careful surgical handling and potentially a low threshold for prophylactic replacement of the ascending aorta that is without additional operative risk in experienced centers. Diagnosis of AAD warrants a mandatory high index of suspicion and depends primarily on imaging. The majority of patients with previous cardiac surgery had no or nonspecific symptoms when AAD was detected. The single most important factor that was associated with a lower operative mortality was implementation of preoperative coronary angiography and appropriate operative management of CAD and graft disease in patients with previous CABG. Because cardiac tamponade and hemodynamic instability are rare (1%), patients with previous cardiac surgery in stable condition should undergo preoperative native coronary and graft status assessment and appropriate operative planning, including aggressive revascularization and the use of deep hypothermic cardiac arrest.
The National Elevation Dataset

The National Elevation Dataset (NED) is a raster product that provides elevation data coverage of the entire United States and its island territories in a seamless format with consistent projection, resolution, elevation units and horizontal and vertical datums. It is the result of the maturation of the U.S. Geological Survey elevation production program, in which national coverage of quadrangle-based digital elevation models has been completed. Specifications and production techniques for the NED are given. The NED fulfills many of the concepts of framework geospatial data as envisioned for the National Spatial Data Infrastructure, allowing users to focus on analysis rather than data preparation. The NED provides basic elevation data for many geographic information system applications and is maintained and updated regularly. The USGS is making several seamless datasets including NED available through the Internet.