Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomics implicates adaptive and innate immunity in Alzheimer's and Parkinson's diseases

Objectives We assessed the current genetic evidence for the involvement of various cell types and tissue types in the aetiology of neurodegenerative diseases, especially in relation to the neuroinflammatory hypothesis of neurodegenerative diseases. Methods We obtained large-scale genome-wide association study (GWAS) summary statistics from Parkinson’s disease (PD), Alzheimer’s disease (AD), and amyotrophic lateral sclerosis (ALS). We used multiple sclerosis (MS), an autoimmune disease of the central nervous system, as a positive control. We applied stratified LD score regression to determine if functional marks for cell type and tissue activity, and gene set lists were enriched for genetic heritability. We compared our results to those from two gene-set enrichment methods (Ingenuity Pathway Analysis and enrichr). Results There were no significant heritability enrichments for annotations marking genes active within brain regions, but there were for annotations marking genes active within cell-types that form part of both the innate and adaptive immune systems. We found this for MS (as expected) and also for AD and PD. The strongest signals were from the adaptive immune system (e.g. T cells) for PD, and from both the adaptive (e.g. T cells) and innate (e.g. CD14: a marker for monocytes, and CD15: a marker for neutrophils) immune systems for AD. Annotations from the liver were also significant for AD. Pathway analysis provided complementary results. Interpretation For Alzheimer’s and Parkinson’s disease, we found significant enrichment of heritability in annotations marking gene activity in immune cells.
Phosphorus in rainwater: Partitioning inputs and impact on the surface coastal ocean

Phosphate concentrations in rainwater were measured at a Ligurian coastal sampling site (Cap Ferrat, France) from February 1997 to February 1998 to study the impact of wet atmospheric phosphorus (P) input on the surface ocean. Soluble and particulate fractions were differentiated to evaluate the atmospheric supply of bioavailable P. Complexed and reactive phases within the dissolved fraction were also separated. Preliminary results showed a high temporal variability in total concentration (0.05–4.3 μmol liter−1). The factors controlling the partitioning between reactive and complexed components are not clear. However, the partitioning between dissolved and particulate fractions is linked to emission sources. Soil‐derived dust from the Sahara was identified as an important source of atmospheric P, mainly insoluble. Conversely, anthropogenic emissions are sources of soluble P (i.e., basically bioavailable). A significant part of these emissions could originate from incinerators and/or biomass burning. The different wet fluxes are calculated to total 165 μmol m−2 yr−1, and the dissolved and particulate inputs are 95 and 70 umol m−2 yr−1, respectively. Taking into account the respective sol ubility of such inputs, anthropogenic emissions appear to be responsible for relatively high amounts of bioavailable P. Even if the atmosphere is globally a minor source of nutrients (compared with riverine inputs and marine vertical mixing), it might be the only source of P in oligotrophic conditions. For example, assuming that P is a limiting factor in the Mediterranean Sea, the rain event of 19 June 1997 (17 μmol m−2 of bioavailable P) potentially induced a new production of 0.02 g C m−2, which is a significant value in such conditions. Converted into biomass and integrated over a 5‐‐thick water layer, such an atmospheric input represents 0.35–0.45 mg chlorophyll a m−2, an appreciable portion of the total biomass during this period. This observation underlines the major role of the atmosphere during oligotrophic periods in the western Mediterranean.
The interaction of temperament and childhood sexual abuse in predicting symptoms of borderline personality disorder

This study examined how two of Rothbart's temperament variables (Rothbart & Derryberry, 1981), negative affect and effortful control, along with childhood sexual abuse, (CSA) predict borderline personality disorder (BPD) symptoms. It was hypothesized that increased negative affect, increased CSA, and their interaction would predict BPD symptoms. It was further hypothesized that this relationship would be mediated by lower levels of effortful control. Questionnaires assessing effortful control, negative affect, CSA, and BPD were administered to 215 female undergraduates. Structural equation modeling supported the first hypothesis, but not the second. The data indicated that the interaction was specific to BPD when compared to avoidant personality disorder. These results provide support for the theory that temperament interacts with the environment to produce BPD.
The Validity of the SmartJump Contact Mat

Abstract Reeve, TC and Tyler, CJ. The validity of the smartjump contact mat. J Strength Cond Res 27(6): 1597–1601, 2013—The aim of this study was to establish the criterion validity of the SmartJump contact mat in assessing vertical jump height (VJH) and peak power (PP). Twenty-three participants (15 men, age = 26 ± 6 years; 8 women, age = 26 ± 9 years) completed a maximal effort vertical jump using 3 different jump types (countermovement jump [CMJ], countermovement with arms [CMJA], and squat jump [SJ]). Data were simultaneously collected on both the contact mat and force platform. Vertical jump height was calculated using the time in air (TIA) method with both force platform (TIAplatform) and contact mat (TIAmat) data and the takeoff velocity (TOV) method using the force platform (TOVplatform) data. Peak power was calculated using a validated equation. The results showed that VJH and PP calculated using the TIAmat method were significantly greater than that calculated from the TIAplatform and TOVplatform methods for all jump types (VJH: p < 0.001, PP: p < 0.001). The results from this study show clear discrepancies between apparatus and calculation methods that may have implications for practitioners and should be considered when assessing VJH and PP in the field.
Feasibility of laparoscopic partial nephrectomy in the obese patient and assessment of predictors of perioperative outcomes

Introduction: Partial nephrectomy is the gold standard for treatment of small renal masses. Our study compares outcomes for obese (body mass index [BMI] ≥30) and healthy (BMI <30) patients undergoing laparoscopic partial nephrectomy (LPN) with the intention of defining preoperative risk factors for complications and renal insufficiency in the obese. Materials and Methods: We conducted a retrospective review of 187 consecutive patients who underwent LPN. We examined the association between BMI and postoperative complication, estimated blood loss (EBL), hospital length of stay, warm ischemic time (WIT), and postoperative renal function. We did similar analyses using the RENAL nephrometry score and the comorbidity status of the patients. Results: We found no statistically significant increase in complications in obese (BMI ≥30) individuals relative to healthy (BMI <30) patients. The obese experienced approximately 100 cc more EBL (P = 0.0111). Patients experienced more complications if they had a Charlson comorbidity score ≥3 (P = 0.0065), an American Association of Anesthesiologists score ≥3 (P = 0.0042), or a history of diabetes mellitus (P = 0.0196). There was no association between RENAL nephrometry score and complication. However, patients with a score ≥8 experienced higher WIT (P = 0.0022), a greater decline in estimated glomerular filtration rate postoperatively (P = 0.0488), and an increased risk of developing chronic kidney disease ≥3 (P = 0.0065). Conclusions: Obese patients undergoing LPN are not at significantly increased risk of complication relative to nonobese patients. Comorbidity status and RENAL nephrometry score, independent of BMI, should be the main considerations of a patient's suitability for LPN.
How Prosecutors Apply the "Federal Prosecutions of Corporations" Charging Policy in the Era of Deferred Prosecutions, and What That Means for the Purposes of the Federal Criminal Sanction

The conference coordinators tasked me with summarizing “how we got here”— that is, to present a brief historical account of the development of current federal corporate law enforcement policy. But to prevent this essay from devolving into a mere recitation of what happened and when, I amended that mission to pursue two further queries: what Department of Justice (“DOJ”) policy tells us about the purposes underlying corporate criminal liability; and whether the DOJ’s application of its policy is likely to effectively serve those purposes. At the outset, I should clarify that these latter questions will not be answered primarily by reference to the voluminous scholarly literature on the question of the goals—and efficacy—of corporate criminal sanctioning. Instead, I focus on what the DOJ perceives to be the purposes of punishment when evaluating whether those purposes are indeed served by federal organizational law enforcement policy as it has developed to date. The reason it makes sense to focus on what prosecutors believe is fairly simple. The standard of liability created over a century of common law adjudication, combined with forces that make it exceedingly difficult for (at least public) corporations to do anything but beg for mercy when the government comes calling, mean that prosecutors, and prosecutors alone, determine what purposes might be served by corporate criminal liability. To support this thesis, I will start with a brief description of the standard of liability and outline a variety of additional forces that make organizational culpability a foregone conclusion in most cases. I believe that my conclusions in this respect reflect popular wisdom in the defense bar, at least. Turning then to the merits, both of my missions first require an inquiry into the guidelines, entitled “Federal Prosecutions of Corporations” (the “Charging Policy”), that the DOJ issued, and has periodically revamped, to guide prosecutors’ discretion. The Charging Policy identifies nine factors that are relevant to three
kHz quasi-periodic oscillations in the low-mass X-ray binary 4U 0614+09

We report on a comprehensive analysis of the kilohertz (≥300 Hz) quasi-periodic oscillations (kHz QPOs) detected from the neutron star low-mass X-ray binary 4U 0614+09 with the Rossi X-ray Timing Explorer. With a much larger data set than previously analysed (all archival data from 1996 February up to 2007 October), we first investigate the reality of the 1330 Hz QPO reported by van-Straaten et al. This QPO would be of particular interest since it has the highest frequency reported for any source. A thorough analysis of the same observation fails to confirm the detection. On the other hand, over our extended data set, the highest QPO frequency we measure for the upper kHz QPO is at ∼1224 Hz; a value which is fully consistent with the maximum values observed in similar systems. Secondly, we demonstrate that the frequency dependence of the quality factor (Q = v/Δv) and amplitude of the lower and upper kHz QPOs follow the systematic trends seen in similar systems. In particular, 4U 0614+09 shows a drop of the quality factor of the lower kHz QPO above ∼700 Hz. If this is due to an approach to the innermost stable circular orbit, it implies a neutron star mass of ∼1.9M ⊙ . Finally, when analysing the data over fixed durations, we have found a gap in the frequency distribution of the upper QPO, associated with a local minimum of its amplitude. A similar gap is not present in the distribution of the lower QPO frequencies, suggesting some cautions when interpreting frequency ratio distributions, based on the occurrence of the lower QPO only.
Recruiting Messages Matter: Message Strategies to Attract Citizen Scientists

Although participation of citizen scientists is critical for a success of citizen science projects (a distinctive form of crowdsourcing), little attention has been paid to what types of messages can effectively recruit citizen scientists. Derived from previous studies on citizen scientists' motivations, we created and sent participants one of four recruiting messages for a new project, Gravity Spy, appealing to different motivations (i.e., learning about science, social proof, contribution to science, and altruism). Counter to earlier studies on motivation, our results showed that messages appealing to learning, contribution and social proof were more effective than a message appealing to altruism. We discuss the inconsistency between the present and prior study results and plans for future work.
Cadmium content of Finnish linseed and estimated consumer intake

�-1 ). The Cd contents of the crush samples were between 0.47 and 1.5 mg kg -1 (mean 0.85 mg kg -1 ). There were differences between the Cd contents of the three examined varieties and years at the experimental farm. Increase in nitrogen fertilization somewhat increased the Cd uptake of linseed. The permitted intake of linseed depends on body weight and on the Cd content of the product and is in most cases higher than the dietary recommendation (24–30 g daily dose of linseed).
Impact of borehole depths on reconstructed estimates of ground surface temperature histories and energy storage

Estimates of ground surface temperature changes and continental energy storage from geothermal data have become well‐accepted indicators of climatic changes. These estimates are independent contributions to the ensemble of paleoclimatic reconstructions and have been used for the validation of general circulation models, and as a component of the energy budget accounting of the global climate system. Recent global and hemispheric analyses of geothermal data were based on data available in the borehole paleoclimatology database, which contains subsurface temperature profiles from a minimum depth of 200 m to about 600 m. Because of the nature of heat conduction, different depth ranges contain the record of past and persistent changes in the energy balance between the lower atmosphere and the ground for different time periods. Here we examine the dependency of estimated ground surface temperature histories and the magnitude of the subsurface heat content on the depth of borehole temperature profiles. Our results show that uncertainties in the estimates of the long‐term surface temperature are in the range of ±0.5K. We conclude that previous estimates of ground surface temperature change remain valid for the period since industrialization, but longer‐term estimates are subject to considerable uncertainties. The subsurface heat content shows a larger range of variability arising from differences in depth of the borehole temperature profiles, as well as from differences in the time of data acquisition, spanning four decades. These results indicate that estimates of subsurface heat should be carried out with caution to decrease cumulative errors in any spatial analysis.
Attention deficit hyperactivity disorder in adults : the latest assessment and treatment strategies

Attention Deficit Hyperactivity Disorder (ADHD) was once considered a childhood disorder that would be outgrown but is now recognized as a disease that can persist into adulthood and even for a lifetime. ADHD in Adults is a quick, easy-to-use reference for practitioners providing critical information about ADHD in adults. Written by the leading authority on ADHD, Dr. Barkley discusses causes, assessment and diagnosis, and treatment options with clear explanations. This essential guide features sidebars, definitions, references, and end-of-chapter key concepts review. ADHD in Adults is a must-have resource for every practitioner caring for adults with ADHD.
NlpI-mediated modulation of outer membrane vesicle production through peptidoglycan dynamics in Escherichia coli

Outer membrane vesicles (OMVs) are ubiquitously secreted from the outer membrane (OM) of Gram‐negative bacteria. These heterogeneous structures are composed of OM filled with periplasmic content from the site of budding. By analyzing mutants that have vesicle production phenotypes, we can gain insight into the mechanism of OMV budding in wild‐type cells, which has thus far remained elusive. In this study, we present data demonstrating that the hypervesiculation phenotype of the nlpI deletion mutant of Escherichia coli correlates with changes in peptidoglycan (PG) dynamics. Our data indicate that in stationary phase cultures the nlpI mutant exhibits increased PG synthesis that is dependent on spr, consistent with a model in which NlpI controls the activity of the PG endopeptidase Spr. In log phase, the nlpI mutation was suppressed by a dacB mutation, suggesting that NlpI regulates penicillin‐binding protein 4 (PBP4) during exponential growth. The data support a model in which NlpI negatively regulates PBP4 activity during log phase, and Spr activity during stationary phase, and that in the absence of NlpI, the cell survives by increasing PG synthesis. Further, the nlpI mutant exhibited a significant decrease in covalent outer membrane (OM‐PG) envelope stabilizing cross‐links, consistent with its high level of OMV production. Based on these results, we propose that one mechanism wild‐type Gram‐negative bacteria can use to modulate vesiculation is by altering PG‐OM cross‐linking via localized modulation of PG degradation and synthesis.
Identification of a Third Human Polyomavirus

ABSTRACT We have previously reported on a system for large-scale molecular virus screening of clinical samples. As part of an effort to systematically search for unrecognized human pathogens, the technology was applied for virus screening of human respiratory tract samples. This resulted in the identification of a previously unknown polyomavirus provisionally named KI polyomavirus. The virus is phylogenetically related to other primate polyomaviruses in the early region of the genome but has very little homology (<30% amino acid identity) to known polyomaviruses in the late region. The virus was found by PCR in 6 (1%) of 637 nasopharyngeal aspirates and in 1 (0.5%) of 192 fecal samples but was not detected in sets of urine and blood samples. Since polyomaviruses have oncogenic potential and may produce severe disease in immunosuppressed individuals, continued searching for the virus in different medical contexts is important. This finding further illustrates how unbiased screening of respiratory tract samples can be used for the discovery of diverse virus types.
Neutral Sulfite Treatment of Lignocellulosic Pulps

Birch and eucalyptus kraft pulps were treated with sulfite solutions in neutral conditions (pH 7) at 170 °C for 60 min and at 190 °C for 180 min. The pulps were analyzed for kappa number, viscosity, carbohydrate composition, and optical properties. Additionally, UV resonance Raman (UVRR) spectroscopy was applied to collect information on the contents of hexenuronic acid (HexA), lignin, and its phenolic hydroxyl groups. The sulfite treatments resulted in (i) depolymerization and partial dissolution of cellulose, (ii) partial dissolution of xylan and substantial decrease in its HexA content, and (iii) removal of the major part of lignin and increase in its phenolic hydroxyl group content. The extensive removal of HexA and depolymerization of cellulose by neutral sulfite were unexpected phenomena that have not been previously reported. According to their degree of polymerization (DP), the pulps were mainly in the form of microcrystalline cellulose after the more drastic treatments.
Land Cover Classification via Multitemporal Spatial Data by Deep Recurrent Neural Networks

Nowadays, modern earth observation programs produce huge volumes of satellite images time series that can be useful to monitor geographical areas through time. How to efficiently analyze such a kind of information is still an open question in the remote sensing field. Recently, deep learning methods proved suitable to deal with remote sensing data mainly for scene classification(i.e., convolutional neural networks on single images) while only very few studies exist involving temporal deep learning approaches [i.e., recurrent neural networks (RNNs)] to deal with remote sensing time series. In this letter, we evaluate the ability of RNNs, in particular, the long short-term memory (LSTM) model, to perform land cover classification considering multitemporal spatial data derived from a time series of satellite images. We carried out experiments on two different data sets considering both pixel-based and object-based classifications. The obtained results show that RNNs are competitive compared with the state-of-the-art classifiers, and may outperform classical approaches in the presence of low represented and/or highly mixed classes. We also show that the alternative feature representation generated by LSTM can improve the performances of standard classifiers.
The role of diaschisis in stroke recovery.

BACKGROUND AND PURPOSE Recovery from hemiparesis after stroke has been shown to involve reorganization in motor and premotor cortical areas. However, whether poststroke recovery also depends on changes in remote brain structures, ie, diaschisis, is as yet unresolved. To address this question, we studied regional cerebral blood flow in 7 patients (mean+/-SD age, 54+/-8 years) after their first hemiparetic stroke. METHODS We analyzed imaging data voxel by voxel using a principal component analysis by which coherent changes in functional networks could be disclosed. Performance was assessed by a motor score and by the finger movement rate during the regional cerebral blood flow measurements. RESULTS The patients had recovered (P<0. 001) from severe hemiparesis after on average 6 months and were able to perform sequential finger movements with the recovered hand. Regional cerebral blood flow at rest differentiated patients and controls (P<0.05) by a network that was affected by the stroke lesion. During blindfolded performance of sequential finger movements, patients were differentiated from controls (P<0.05) by a recovery-related network and a movement-control network. These networks were spatially incongruent, involving motor, sensory, and visual cortex of both cerebral hemispheres, the basal ganglia, thalamus, and cerebellum. The lesion-affected and recovery-related networks overlapped in the contralesional thalamus and extrastriate occipital cortex. CONCLUSIONS Motor recovery after hemiparetic brain infarction is subserved by brain structures in locations remote from the stroke lesion. The topographic overlap of the lesion-affected and recovery-related networks suggests that diaschisis may play a critical role in stroke recovery.
Rate constants rather than biochemical mechanism determine behaviour of genetic clocks

Many biological systems contain both positive and negative feedbacks. These are often classified as resonators or integrators. Resonators respond preferentially to oscillating signals of a particular frequency. Integrators, on the other hand, accumulate a response to signals. Computational neuroscientists often refer to neurons showing integrator properties as type I neurons and those showing resonator properties as type II neurons. Guantes & Poyatos have shown that type I or type II behaviour can be seen in genetic clocks. They argue that when negative feedback occurs through transcription regulation and post-translationally, genetic clocks act as integrators and resonators, respectively. Here we show that either behaviour can be seen with either design and in a wide range of genetic clocks. This highlights the importance of parameters rather than biochemical mechanism in determining the system behaviour.