Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the ability of end-point methods to predict the binding affinity tendency of protein kinase inhibitors

Because of the high economic cost of exploring the experimental impact of mutations occurring in kinase proteins, computational approaches have been employed as alternative methods for evaluating the structural and energetic aspects of kinase mutations. Among the main computational methods used to explore the affinity linked to kinase mutations are docking procedures and molecular dynamics (MD) simulations combined with end-point methods or alchemical methods. Although it is known that end-point methods are not able to reproduce experimental binding free energy (ΔG) values, it is also true that they are able to discriminate between a better or a worse ligand through the estimation of ΔG. In this contribution, we selected ten wild-type and mutant cocrystallized EGFR–inhibitor complexes containing experimental binding affinities to evaluate whether MMGBSA or MMPBSA approaches can predict the differences in affinity between the wild type and mutants forming a complex with a similar inhibitor. Our results show that a long MD simulation (the last 50 ns of a 100 ns-long MD simulation) using the MMGBSA method without considering the entropic components reproduced the experimental affinity tendency with a Pearson correlation coefficient of 0.779 and an R2 value of 0.606. On the other hand, the correlation between theoretical and experimental ΔΔG values indicates that the MMGBSA and MMPBSA methods are helpful for obtaining a good correlation using a short rather than a long simulation period.
Typology and correlates of parental stress among caregivers of children with DBDs in low-resourced communities in Uganda

Disruptive Behavior Disorders (DBDs) is one of the most common mental health problems among children in Uganda and SSA. Yet, to our knowledge no research has studied parenting stress (PS) among caregivers of children with DBDs, or investigated which risk factors originate from the child, parent, and contextual environment. Using a rigorous analytical approach, we aimed to: 1) identify different types and; 2) examine factors associated with PS and how correlates differ according to the type of stress experienced among caregivers of children with DBDs in low-resourced Ugandan communities. We used data from 633 caregivers of children with DBDs from SMART-Africa Uganda study. PS, was measured using the 36-item Parenting Stress Index-Short Form (PSI-SF). To identify focal correlates related to child/parent/contextual environment, we performed variable importance screening using the Stata command -gvselect- and specified mixed/melogit multilevel modeling with random effects. Secondly, focal correlates were included in the cross-fit partialing out lasso linear/logistic regression (double machine-learning) model. Caregivers mostly experienced stress from parental distress and caring for a child with difficult behavior. As scores increased by one unit on: caregiver mental health distress, PSI-SF increased by 0.23 (95% CI = 0.15, 0.32) (reflecting higher stress levels); Child difficulties, PSI-SF increased by 0.77 (95% CI = 0.52, 1.02). Contrastingly, for every one unit increase in family cohesion scores, PSI-SF decreased by 0.54 (95% CI = -0.84, -0.23). Caregivers with college/diploma/undergraduate/graduate education had less stress than those completing primary only or never attended school [Coefficient = -8.06 (95% CI = -12.56, -3.56)]. Family financial supporters had significantly higher Parental distress than caregivers who were not [Coefficient = 2.68 (95% CI = 1.20, 4.16)]. In low-resource settings like Uganda where mental health support is limited, community-based family-focused and economic empowerment interventions that improve community support systems and address financial barriers can reduce stress levels of caregivers of children with DBDs.
Experimental study of the penetration of oxygen and deuterium atoms into porous water ice

Context. Many interstellar molecules are thought to form on dust grains. In particular, hydrogenation is one of the major mechanisms of the formation of mantle ice. To date it is not clear if H atoms can penetrate the bulk of the ice mantle or if it only has chemical activity on the accessible surface of grains. Aims. We wish to study the efficiency of atoms deposited on the outer surface of the amorphous solid water to penetrate into the ice bulk. Methods. NO molecules react with O and H atoms. They are easily detected by infrared (IR) spectroscopy. These two properties make this molecule an ideal chemical tracer for the penetration of O and H atoms through water ice. In our experiments we first deposited a NO undercoat and covered this layer (at 40 K) with a variable amount of water ice. Then, we exposed this undercoat to D (10 K) or O (40 K) atoms, and we followed the NO consumption and the products that appeared via IR signatures, and we finally analyzed the desorption of all species through a temperature-programmed desorption technique. We experimentally characterize the accessible surface of the ice and provide a model to interpret quantitatively our measurements. Results. Water ice limits the destruction of tracer NO molecules. The thicker the ice, the more NO remains unreacted. H and O atoms lead to the same amount of NO consumption, pointing out that access to reactants for these two different atoms is identical. We discuss different possible scenarios of NO localization (in and/or on the ice) and determine how this affects our observables (IR data and desorption profiles). Conclusions. In our experimental conditions, it is not possible to measure any atom penetration through the bulk of the ice. The surface diffusion followed by reaction with NO or by self-reaction (i.e., H + H → H2) is faster than bulk diffusion. We propose lower limit values for penetration barriers. Therefore the building of astrophysical ice mantles should be mostly driven by surface reactivity.
Determination of wind from NIMBUS 6 satellite sounding data

Abstract : Objective methods of computing upper-level and surface wind fields from Nimbus-6 satellite sounding data are developed. These methods are evaluated by comparing satellite-derived and rawinsonde wind fields on gridded constant-pressure charts in four geographical regions. Satellite-derived and hourly observed surface wind fields are compared. Results indicate that the best satellite-derived wind on constant-pressure charts is a geostrophic wind derived from highly smoothed fields of geopotential height. Satellite-derived winds computed in this manner and rawinsonde winds show similar circulation patterns except in areas of small height gradients. Magnitudes of the standard deviation of the differences between satellite-derived and rawinsonde wind speeds range from approximately 3 to 12 m/s on constant-pressure charts and peak at the jet-stream level. Fields of satellite-derived surface wind computed with the logarithmic wind law agree well with fields of observed surface wind in most regions. Magnitudes of the standard deviation of the difference in surface wind speed range from approximately 2 to 4 m/s, and satellite-derived surface winds are able to depict flow across a cold front and around a low-pressure center.
A bioarchaeological perspective on Wari imperialism in the Andes of Peru : a view from heartland and hinterland skeletal populations

Tiffiny A. Tung (Under the direction of Clark Spencer Larsen and Brian R. Billman) This dissertation uses bioarchaeological data from three skeletal populations to evaluate the impact of Wari imperialism on heartland and hinterland communities during the Middle Horizon Period (AD 550 1000) in the Andes of Peru. It is hypothesized that Wari conquest contributed to different levels of morbidity, violent injury, and distinct forms of community organization and ritual practices among communities from the site of Conchopata (Wari heartland) and Beringa and La Real (Wari hinterland). This hypothesis is tested through analysis of human skeletal remains, archaeological context, and comparisons to other Andean skeletal populations. Differences in community organization are reconstructed through age-at-death and sex profiles. Patterns of morbidity are assessed by observing for skeletal lesions indicative of childhood iron deficiency anemia. Injury morbidity and mortality patterns related to violent interactions are examined by documenting the frequency and patterning of cranial depression fractures, “parry” fractures, and peri-mortem trauma. Wari ritual practices are evaluated through analysis of human trophy heads and their associated ritual contexts. Finally, strontium isotope data from burials and trophy heads from Conchopata are evaluated to determine if they were natal members or immigrants and if the trophy head victims were from the local or foreign region. This study demonstrates that the demographic composition of the three populations were significantly different, suggesting that the communities were structured in distinct Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.
Modeling Saltmarsh Sparrow Distribution in Connecticut

Remote sensing data can represent various habitat characteristics, and can thus replace detailed ground sampling in the construction of habitat models. Remote sensing data may also distinguish additional variation in conditions that can be useful in discriminating presence and absence of species. To predict saltmarsh sparrow distribution and nesting activity in Connecticut salt marshes, I compared a set of Bayesian hierarchical models in which variables were generated from field or remote sensing data, at a scale of 1-ha plots and at the landscape scale. Field data consisted of plant structure and plant composition variables. Data derived from remote sensing included high and low marsh classifications, LiDAR elevation data, and a classification derived from spectral characteristics specifically associated with saltmarsh sparrow presence or absence. The best sparrow presence model used a variable derived from raw spectral reflectance values associated with plots where sparrows did not occur, indicating that the remote sensing data included additional information about marsh conditions associated with saltmarsh sparrow presence and absence than was detected using plant composition, structure, or community classes. Nest presence, in contrast, was modeled best using vegetation structure variables that required data collection on the ground. Saltmarsh sparrow presence, therefore, will not necessarily indicate that an area provides all conditions suitable for reproduction and persistence.
Trust based attachment

In social systems subject to indirect reciprocity, a positive reputation is key for increasing one’s likelihood of future positive interactions [1–13]. The flow of gossip can amplify the impact of a person’s actions on their reputation depending on how widely it spreads across the social network, which leads to a percolation problem [14]. To quantify this notion, we calculate the expected number of individuals, the “audience”, who find out about a particular interaction. For a potential donor, a larger audience constitutes higher reputational stakes, and thus a higher incentive, to perform “good” actions in line with current social norms [7, 15]. For a receiver, a larger audience therefore increases the trust that the partner will be cooperative. This idea can be used for an algorithm that generates social networks, which we call trust based attachment (TBA). TBA produces graphs that share crucial quantitative properties with real-world networks, such as high clustering, small-world behavior, and powerlaw degree distributions [16–21]. We also show that TBA can be approximated by simple friend-of-friend routines based on triadic closure, which are known to be highly effective at generating realistic social network structures [19, 22–25]. Therefore, our work provides a new justification for triadic closure in social contexts based on notions of trust, gossip, and social information spread. These factors are thus identified as potential significant influences on how humans form social ties.
Modelling the spatial distribution of actual terrestrial evapotranspiration using a hydrological and meteorological approach

Terrestrial evapotranspiration (TET) plays an important role in determining water balance and heat balance in a water cycle between land surface and atmosphere. In this paper a dynamic approach based on the integration of meteorological and hydrological methods was proposed for simulating actual TET distribution across large spatial and temporal extents by reflecting the impacts of climate, complex land cover features, and the movement characteristics of soil moisture upon actual TET. The proposed approach was then used to simulate the actual TET in China. The distribution characteristics of actual TET demonstrate that the TET in eastern China is larger than that in western China, and the actual TET in the region with low latitude is larger than that with high latitude in the context of China. From 1991 to 1995 and 2000, actual monthly and annual TET in most regions show an increasing trend within the 10-year horizon, especially in arid and semiarid regions.
Quantum key distribution system operating at sifted-key rate over 4 Mbit/s

A complete fiber-based polarization encoding quantum key distribution (QKD) system based on the BB84 protocol has been developed at National Institute of Standard and Technology (NIST). The system can be operated at a sifted key rate of more than 4 Mbit/s over optical fiber of length 1 km and mean photon number 0.1. The quantum channel uses 850 nm photons from attenuated high speed VCSELs and the classical channel uses 1550 nm light from normal commercial coarse wavelength division multiplexing devices. Sifted-key rates and quantum error rates at different transmission rates are measured as a function of distance (fiber length). A polarization auto-compensation module has been developed and utilized to recover the polarization state and to compensate for temporal drift. An automatic timing alignment device has also been developed to quickly handle the initial configuration of quantum channels so that detection events fall into the correct timing window. These automated functions make the system more practical for integration into existing optical local area networks.
Quality of hematology and clinical chemistry results in laboratory and zoo nonhuman primates: Effects of the preanalytical phase. A review

Most errors in clinical pathology originate in the preanalytical phase, which includes all steps from the preparation of animals and equipment to the collection of the specimen and its management until analyzed. Blood is the most common specimen collected in nonhuman primates. Other specimens collected include urine, saliva, feces, and hair. The primary concern is the variability of blood hematology and biochemistry results due to sampling conditions with the effects of capture, restraint, and/or anesthesia. Housing and diet have fewer effects, with the exception of food restriction to reduce obesity. There has been less investigation regarding the impact of sampling conditions of nonblood specimens.
Manifold Learning in Medical Imaging

Manifold learning theory has seen a surge of interest in the modeling of large and exten- sive datasets in medical imaging since they capture the essence of data in a way that fundamentally outperforms linear methodologies, the purpose of which is to essentially describe things that are flat. This problematic is particularly relevant with medical imaging data, where linear techniques are frequently unsuitable for capturing variations in anatomical structures. In many cases, there is enough structure in the data (CT, MRI, ultrasound) so a lower dimensional object can describe the degrees of freedom, such as in a manifold structure. Still, complex, multivariate distributions tend to demonstrate highly variable structural topologies that are impossible to capture with a single manifold learn- ing algorithm. This chapter will present recent techniques developed in manifold theory for medical imaging analysis, to allow for statistical organ shape modeling, image seg- mentation and registration from the concept of navigation of manifolds, classification, as well as disease prediction models based on discriminant manifolds. We will present the theoretical basis of these works, with illustrative results on their applications from various organs and pathologies, including neurodegenerative diseases and spinal deformities. The proposed model provides a way to analyze longitudinal samples from a geodesic curve in manifold space, thus simplifying the mixed effects when studying group-average trajectories.
Pengaplikasian Sensor Hujan dan LDR untuk Lampu Mobil Otomatis Berbasis Arduino Uno

Pesatnya perkembangan teknologi mendorong sektor industri untuk lebih kreatif dalam membuat sebuah alat sederhana yang dapat membantu masyarakat dalam kehidupan sehari-hari, salah satunya pada lampu kendaraan. Dalam rangka mengembangkan teknologi pada lampu kendaraan untuk mengurangi peluang terjadinya kecelakaan, dilakukan pengaplikasian sensor hujan dan sensor cahaya pada lampu mobil secara otomatis berbasis Arduino sehingga mempermudah pemakaian lampu pada kendaraan, terutama untuk kemajuan industri mobil. Sensor LDR (Light Dependent Resistor) dan sensor hujan digunakan untuk memberikan informasi kepada Arduino sehingga lampu pada bagian depan dan belakang mobil akan menyala secara otomatis.
Trained immunity of alveolar macrophages enhances injury resolution via KLF4-MERTK-mediated efferocytosis

Chakraborty et al. demonstrate that a subset of tissue-resident alveolar macrophages shows greater capacity for efferocytosis and prevents hyperinflammation following repeated pathogen challenges. These trained alveolar macrophages exhibit upregulation of the efferocytosis receptor MERTK mediated by the transcription factor KLF4.
Review of ethics for occupational hygiene hazard monitoring surveys using sensors

Abstract This review is about the ethical use of sensors to monitor occupational exposure to hazards. It considers whether the same or different, ethical measures apply to using sensors, compared to conventional hazard monitoring surveys. To undertake the review, subject experts developed a research question, identified suitable search terms, and set the scope of these searches. Candidate research papers dating from 2000 to mid-2022 that met inclusion criteria were identified and reviewed by each author. Ethical concerns were identified by the authors of studies in which sensors were used to monitor employee health and well-being, but most of the studies that used them to monitor employee exposure to hazards focused on the technical aspects of their deployment. These ethical concerns included questions about employee rights and privacy, the anonymity of the data collected with sensors, and how the security of this data is managed. The review considers ethical standards and codes of practice for occupational hygiene work and the ethical risks when sensors are used to gather data. Sensors may provide insight into occupational exposure to hazards, but their use is not always adequately explained to employees by those managing this monitoring work. The ethical concerns identified were relevant to many areas of industrial hygiene work, but more studies are required that consider the ethical use of sensors in workplaces. Studies that monitored employee health, well-being, and productivity, identified ethical risks in using sensors to monitor these endpoints. An ethical framework and checklist for hygienists are proposed including a set of questions that consider the risks of using sensors to monitor occupational hazards. Industrial hygiene professional bodies provide ethical codes of practice for their members but may also need to consider the implications of using sensors in workplaces. Ethical standards support the collection of industrial hygiene exposure data whilst maintaining the privacy rights of employees.
Principles of stratigraphic analysis

Accumulating stratigraphic data sedimentary textures, mineralogies and structures completeness of the stratigraphic record geologic time and correlation patterns in the distribution of organisms evolution and biostratigraphy depositional environments and facies I - continental environments depositional environments and facies II - transitional environments depositional environments and facies III - marine environments lithostratigraphy physical framework for stratigraphic analysis economic stratigraphy I - primary deposits economic stratigraphy II - deposits formed by secondary mineralization.
Application et modélisation du principe de la précontrainte sur des assemblages de structure bois

Dans un assemblage precontraint, des efforts sont transmis entre les pieces par mobilisation du frottement suite a l'application d'une contrainte de compression normale. L'objectif de ce travail etait de transposer ce principe de transmission des efforts au materiau bois. A partir de resultats existants, une etude experimentale preliminaire a ete menee sur des chaumes de bambou. L'interet de cette « graminee » par rapport au bois est sa resistance importante en compression transversale. Pour appliquer ce principe a des avives de bois, il a ete necessaire de les densifier par compression localisee a froid au-dela de leur limite elastique. Une caracterisation de Picea abies en compression transversale au-dela de sa limite elastique a ete realisee. Cette analyse a abouti a une loi de comportement fonction de la densite de l'eprouvette. De plus, l'influence de la densification du bois sur sa resistance en traction longitudinale a ete mesuree. Il s'avere que cette resistance est constante puis chute a partir d'un taux de densification critique fonction de la masse volumique du bois. La phase de mise en place de la precontrainte dans les assemblages bois et bambou testes a ete modelisee par elements finis. L'orthotropie des materiaux a ete pris en compte par la superposition d'un modele mousse (comportement non-lineaire transversal) et d'un modele poutre (direction longitudinale) creant une structure dont la taille des elements ne descend pas en dessous de celle des cernes. Ce modele structural mesoscopique a permis de simuler les phases de densification, charge, decharge de l'assemblage et d'atteindre la limite a rupture, permettant d'aller jusqu'a une demarche d'optimisation.
The SYNOP Experiment. Inverted Echo Sounder Data Report for October 1987 to May 1988

Abstract : The Synoptic Ocean Prediction experiment (SYNOP) was undertaken with the goal that increased understanding other Gulf Stream obtained through coordinated observations could be integrated with numerical models, including predictive models of the Gulf Stream. Our moored experiment, which began in fall of 1987, consists of two separate arrays in the Gulf Stream. The Inlet array consists of inverted echo sounders (IES) and deep current meters in a 120 x 150 km rectangle Cape Hatteras. It measures key parameters that describe the variability of the Gulf Stream and deep western boundary current (DWBC) near. In this region the Gulf first flows into deeper water and crosses over the DWBC. The Central array of IESs, a 300x320 km rectangle centered on the Gulf Stream near 68W, monitors the thermocline structure of the Gulf Stream in the region of large meanders and frequent interactions with rings. IES data are documented here by plots and tables of basic statistics and pertinent deployment information. Altogether 22 IES records are presented, plus pressure and temperature records a 5 sites. The plots are time series of measured travel time, pressure, and temperature; the residual pressure; and low-pass filtered records of residual pressure, thermocline depth, and temperature. Keywords: Echo; Sounders; Pressure; Sensors; Gulf Stream; Ocean currents.