jimnoneill/paper-to-field-training huggingface dataset:
Causal inference for data subject to non-compliance and missing values.

Non-compliance is very common in randomized experiments involving human participants. The intent-to-treat method and the as-treated method are two common methods for estimating treatment effects in randomized experiments, but both have limitations. The intent-to-treatment method estimates the effect of treatment allocation rather than the treatment itself, and the as-treated method is subject to selection bias. Rubin causal model (RCM) provides a useful alternative way to analyze the data subject to non-compliance. The parameter of interest in the RCM approach is the treatment effect for the sub-population of compliers, called the Complier-Average Causal Effect (CACE). In addition to non-compliance, the existence of missing values in the outcome and the baseline covariates further complicates the data analysis. Under Rubin Causal Model framework, this dissertation develops new models for causal inference from experiments subject to non-compliance and missing values. Two problems are considered: (1) Inference for the CACE for discrete outcomes with non-compliance and missing values only in the outcomes; (2) Inference for the CACE for discrete or continuous outcomes with non-compliance and missing values in the outcomes and the covariates. A non-hierarchical form of loglinear models (Agresti, 1990; McCullagh and Nelder, 1989) is proposed for the first problem, and an extension of the general location model (Olkin and Tate, 1961; Little and Schluchter, 1985) is proposed for the second problem. Models are developed for both ignorable and latent ignorable missing data mechanisms as described in Frangakis and Rubin (1999). Inferences under these models are developed based on EM algorithms and Bayesian Markov-chain Monte Carlo methods. In addition, simulation studies are carried out comparing the likelihood-based approaches in this dissertation with existing methods, specifically the instrumental variable methods in social science literature. Sensitivity of the inference to model assumptions and the influence of missing data mechanisms are also investigated by simulations. Based on the simulation studies, likelihood-based methods appear to be more efficient than IV methods, and inferences for the CACE appear to be quite robust to lack of normality of the distribution of continuous outcomes for both likelihood-based and IV approaches. Results of the IV methods and the likelihood-based methods for binary outcomes are more sensitive to misspecification of the probit model. The proposed methods are applied to data from a Job Search prevention intervention for unemployed workers which motivated this research, and the intervention helps to increase the re-employment rate among compliers.

Topic: Bayesian Modeling and Causal Inference
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Effects of Sound-Pressure Change on the 40 Hz Auditory Steady-State Response and Change-Related Cerebral Response

The auditory steady-state response (ASSR) elicited by a periodic sound stimulus is a neural oscillation recorded by magnetoencephalography (MEG), which is phase-locked to the repeated sound stimuli. This ASSR phase alternates after an abrupt change in the feature of a periodic sound stimulus and returns to its steady-state value. An abrupt change also elicits a MEG component peaking at approximately 100–180 ms (called “Change-N1m”). We investigated whether both the ASSR phase deviation and Change-N1m were affected by the magnitude of change in sound pressure. The ASSR and Change-N1m to 40 Hz click-trains (1000 ms duration, 70 dB), with and without an abrupt change (± 5, ± 10, or ± 15 dB) were recorded in ten healthy subjects. We used the source strength waveforms obtained by a two-dipole model for measurement of the ASSR phase deviation and Change-N1m values (peak amplitude and latency). As the magnitude of change increased, Change-N1m increased in amplitude and decreased in latency. Similarly, ASSR phase deviation depended on the magnitude of sound-pressure change. Thus, we suspect that both Change-N1m and the ASSR phase deviation reflect the sensitivity of the brain’s neural change-detection system.

Topic: Neural dynamics and brain function
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Geometallurgical modelling techniques applicable to pre-feasibility projects: La Colosa case study

La Colosa is a world-class porphyry Au project located in Colombia, currently undergoing pre-feasibility analysis. As part of collaboration between AngloGold Ashanti and the AMIRA P843A GeMIII Project, the application of emerging geometallurgical characterisation testing and modelling tools has been incorporated in early stages of project development. The aim of the geometallurgical study is to map inherent comminution variability across the La Colosa deposit providing information critical for mine/mill design and optimisation. In this study, site-based data incorporating multi-element assays, QXRD bulk mineralogy measurements, EQUOtip rebound hardness data, and routine geological logging information from 59 diamond drill holes has been integrated with a range of geometallurgically specific comminution test (i.e. GeMCi, A*b, BMWi). The work in this paper demonstrates the integration techniques used at La Colosa to link routine data acquisition methods with comminution test results through the development of proxy support models. The integration incorporates a range of statistical techniques including principal component analysis and regression modelling. By creating proxy models, comminution index estimates can be propagated into the geological database enabling comminution processing domains to be defined. These domains provide the first spatial representation of comminution performance and variability at La Colosa and can be compared against traditional geological domains. This study provides the foundation for ongoing comminution characterisation as the La Colosa project evolves through project cycles into an operational mine.

Topic: Mineral Processing and Grinding
Subfield: Mechanical Engineering
Field: Engineering
Domain: Physical Sciences
Peer Influence and School Library Use by Students in Public Secondary Schools in Lagos State, Nigeria

&#x0D; &#x0D; &#x0D; This study investigated the influence of peer influence on school library use among public secondary schools in Lagos State, Nigeria. The study adopted survey research design. The study population comprised 16,366 students in public secondary schools in Lagos State. Structured questionnaire was used for the data collection and the Cronbach alpha value ranged from 0.7 to 0.9 which shows that the instrument is valid. Findings showed that students in public secondary schools in Lagos State, Nigeria used school library twice a week (mean = 3.00, SD = 0.79). School library was used daily among students in public secondary schools in Lagos State, in order to enable them to study and perform well in their studies (x̅ = 3.33). The extent of peer influence on library use was moderately high (the mean = 2.91, SD = 0.86). Peer pressure exerted high influence at (x̅ = 3.05) and peer academic value at mean = 2.76. Peer influence has a negative significant influence on school library use among students in public secondary schools in Lagos State, Nigeria (R2 = 0.025, β = -0.157, t = -5.781, p&lt;0.05). Therefore, this study recommends that school administrators and librarian should care for each student in situation where there is negative influence it should be observed and corrected before it becomes a public menace.&#x0D; &#x0D; &#x0D;

Topic: Library Science and Information Literacy
Subfield: Library and Information Sciences
Field: Social Sciences
Domain: Social Sciences
Herbicidal efficacy of some natural products and mulching compared to herbicides for weed control in onion fields

In two field experiments, the effect of some weed control treatments (citric acid at the rate of 10, 15 and 20%, acetic acid at the rate of 20, 30 and 40%, oxadiargyl, oxyflurfen, rice straw mulch, hand hoeing and an unweeded check control treatment) on weed growth and onion productivity in sandy soils at the Agricultural Experimental Station of the National Research Centre, Egypt was studied. The results indicated that all weeded treatments reduced the dry weight of broadleaf, grassy and total weeds as compared with the weedy check. Oxadiargyl, followed by two hand hoeing, rice straw mulch and acetic acid 40% recorded the greatest weed control efficiency. Insignificant differences were noticed between these treatments. Applying rice straw mulch increased bulb length, bulb diameter, bulb weight and onion yield by 67.52, 57.55, 45.74 and 66.22% over the weedy check, respectively. The highest values of N, P and K were obtained from rice straw mulch treatment followed by hand hoeing, oxadiargyl and acetic acid 40% treatments. It may be concluded that farmers can certainly depend on mulching or acetic acid at 40% instead of using chemical herbicides especially in organic farm systems for controlling onion weeds.

Topic: Allelopathy and phytotoxic interactions
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Data from Tumor-Produced Interleukin-8 Attracts Human Myeloid-Derived Suppressor Cells and Elicits Extrusion of Neutrophil Extracellular Traps (NETs)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Myeloid-derived suppressor cells (MDSC) are considered an important T-cell immunosuppressive component in cancer-bearing hosts. The factors that attract these cells to the tumor microenvironment are poorly understood. IL8 (CXCL8) is a potent chemotactic factor for neutrophils and monocytes.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; MDSC were characterized and sorted by multicolor flow cytometry on ficoll-gradient isolated blood leucokytes from healthy volunteers (&lt;i&gt;n&lt;/i&gt; = 10) and advanced cancer patients (&lt;i&gt;n&lt;/i&gt; = 28). In chemotaxis assays, sorted granulocytic and monocytic MDSC were tested in response to recombinant IL8, IL8 derived from cancer cell lines, and patient sera. Neutrophil extracellular traps (NETs) formation was assessed by confocal microscopy, fluorimetry, and time-lapse fluorescence confocal microscopy on short-term MDSC cultures.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; IL8 chemoattracts both granulocytic (GrMDSC) and monocytic (MoMDSC) human MDSC. Monocytic but not granulocytic MDSC exerted a suppressor activity on the proliferation of autologous T cells isolated from the circulation of cancer patients. IL8 did not modify the T-cell suppressor activity of human MDSC. However, IL8 induced the formation of NETs in the GrMDSC subset.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; IL8 derived from tumors contributes to the chemotactic recruitment of MDSC and to their functional control. &lt;i&gt;Clin Cancer Res; 22(15); 3924–36. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Topic: Immune cells in cancer
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
An Approximation Algorithm for the Bipartite Traveling Tournament Problem

The bipartite traveling tournament problem (BTTP) is an NP-complete scheduling problem whose solution is a double round-robin inter-league tournament with minimum total travel distance. The 2n-team BTTP is a variant of the well-known traveling salesman problem (TSP), albeit much harder as it involves the simultaneous coordination of 2n teams playing a sequence of home and away games under fixed constraints, rather than a single entity passing through the locations corresponding to the teams' home venues. As the BTTP requires a distance-optimal schedule linking venues in close proximity, we provide an approximation algorithm for the BTTP based on an approximate solution to the corresponding TSP. We prove that our polynomial-time algorithm generates a 2n-team inter-league tournament schedule whose total distance is at most 1 + 2c/3 + (3 − c)/(3n) times the total distance of the optimal BTTP solution, where c is the approximation factor of the TSP. In practice, the actual approximation factor is far better; we provide a specific example by generating a nearly-optimal inter-league tournament for the 30-team National Basketball Association, with total travel distance just 1.06 times the trivial theoretical lower bound.

Topic: Scheduling and Timetabling Solutions
Subfield: Management Science and Operations Research
Field: Decision Sciences
Domain: Social Sciences
A pilot spectroscopy study on time-varying bioimpedance during electrically-induced muscle contraction

Alterations in the health of muscles can be evaluated through the use of electrical impedance myography (EIM). To date, however, nearly all work has relied upon single-frequency/spectroscopy stepped-sine measurements of static muscle (contracted or relaxed). In this work, we assessed the temporal alterations in the impedance spectrum (1 kHz to 1 MHz) behavior of gastrocnemius during the active process of muscle contraction. The approach is based on the multisine impedance spectroscopy technique. The gastrocnemii of a wild type mouse was measured during electrically-induced muscle contraction via direct current stimulation of the sciatic nerve. The processes of contraction and relaxation were clearly identified in the time-frequency impedance spectrum likely corresponding to an increase muscle fiber diameter. The technique of dynamic multisine EIM has the potential of providing useful insights into contractile mechanisms of muscle in health and disease.

Topic: Muscle activation and electromyography studies
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
Global Analysis of the Differences Between the MODIS Vegetation Index Compositing Date and the Actual Acquisition Date

Image compositing enables the generation of continuous and equidistant time series of vegetation indices (VIs) as a requisite for deriving phenological metrics. This is achieved by selecting a representative choice from available observations within a compositing period. Commonly, phenological processors associate the VI value with a reference date rather than the actual acquisition date. This letter focuses on a global assessment of the resulting temporal discrepancy between the assumed reference date and the actual acquisition date using Moderate Resolution Imaging Spectroradiometer (MODIS)-VI day of composite (DOC) information from 2000 to 2015. It is shown that the long-term global mean DOC coincides with the midday of a compositing period (day 8.44 ± 0.44). The global summarized 2-D frequency distributions of succeeding compositing periods revealed that only 16.93% of all occurrences indicate a 16-day difference. The commonly used assumptions that the DOC coincides with the first, mid, or last day of the compositing period on average only hold true for 7.02%, 6.07%, and 6.03% of temporal succeeding compositing periods, respectively. Spatial patterns of 2-D frequency distributions occur as a result of climatic regions and seasonality. A MODIS tile is on average composed of more than 50% DOC combinations, indicating deviations (1–31 days) from the 16-day difference. Since information about the actual acquisition date is available, and methods for the incorporation of irregular data into phenological analysis do exist, it is recommended to incorporate this information into the phenology research based on VI time series to avoid unnecessary uncertainty.

Topic: Remote Sensing in Agriculture
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Barbatula altayensis: Bogutskaya, N. &amp; Rema Devi, K.R.

Established in 1964, the IUCN Red List of Threatened Species has evolved to become the world’s most comprehensive information source on the global conservation status of animal, fungi and plant species.

Topic: Coleoptera: Cerambycidae studies
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
[POSTER] 2D-3D Co-segmentation for AR-based Remote Collaboration

In Augmented Reality (AR) based remote collaboration, a remote user can draw a 2D annotation that emphasizes an object of interest to guide a local user accomplishing a task. This annotation is typically performed only once and then sticks to the selected object in the local user's view, independent of his or her camera movement. In this paper, we present an algorithm to segment the selected object, including its occluded surfaces, such that the 2D selection can be appropriately interpreted in 3D and rendered as a useful AR annotation even when the local user moves and significantly changes the viewpoint.

Topic: Augmented Reality Applications
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
A passion for the science of the human genome

The complete sequencing of the human genome introduced a new knowledge base for decoding information structured in DNA sequence variation. My research is predicated on the supposition that the genome is the most sophisticated knowledge system known, as evidenced by the exquisite information it encodes on biochemical pathways and molecular processes underlying the biology of health and disease. Also, as a living legacy of human origins, migrations, adaptations, and identity, the genome communicates through the complexity of sequence variation expressed in population diversity. As a biomedical research scientist and academician, a question I am often asked is: “How is it that a black woman like you went to the University of Michigan for a PhD in Human Genetics?” As the ASCB 2012 E. E. Just Lecturer, I am honored and privileged to respond to this question in this essay on the science of the human genome and my career perspectives.

Topic: Race, Genetics, and Society
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
A Daily Rhythm in Glucose Tolerance

The suprachiasmatic nucleus (SCN), the biological clock, is responsible for a 24-h rhythm in plasma glucose concentrations, with the highest concentrations toward the beginning of the activity period. To investigate whether the SCN is also responsible for daily fluctuations in glucose uptake and to examine how these fluctuations relate to the rhythm in plasma glucose concentrations, SCN-intact rats and SCN-lesioned rats were injected intravenously with a glucose bolus at different time points. We found an increase in glucose uptake toward the beginning of the activity period, followed by a gradual reduction in glucose uptake toward the end of the activity period. The daily variation in glucose tolerance seemed not to be caused by fluctuations in insulin responses of the pancreas but by a daily variation in insulin sensitivity. Lesioning the SCN resulted in the disappearance of the daily fluctuation in glucose uptake and insulin sensitivity. Interestingly, SCN-lesioned rats showed an enhancement in glucose tolerance that could not be explained by higher insulin responses or enhanced insulin sensitivity. Therefore, these findings suggest a role for the SCN in insulin-independent glucose uptake. The present results further show that the daily rhythm in glucose tolerance follows the same pattern as the daily rhythm in plasma glucose concentrations. We hypothesized that the biological clock prepares the individual for the upcoming activity period by two separate mechanisms: increasing plasma glucose concentrations and making tissue more tolerant to glucose.

Topic: Circadian rhythm and melatonin
Subfield: Endocrine and Autonomic Systems
Field: Neuroscience
Domain: Life Sciences
CLAREAMENTO DENTAL EM PACIENTES COM HIPERSENSIBILIDADE: SÉRIE DE CASOS

The possibility of pain resultant from tooth bleaching can limit the indication of this treatment in patients with pre-existing dentin hypersensitivity. Purpose: To provide a case series with alternatives for tooth bleaching that might reduce the pos-operative sensibility. Description of cases: Three patients with dentin sensitivity and complaining of tooth discoloration were selected. For each patient, a technique for tooth bleaching was randomly selected; using 15-35% hydrogen peroxide, and application of an desensitizing agent before or after the bleaching (toothpaste or 2% potassium nitrate). Conclusion: Bleaching was successfully performed in the three clinical cases. However, the previous desensitization using the toothpaste resulted in greater comfort for the patient.

Topic: Dental Erosion and Treatment
Subfield: Orthodontics
Field: Dentistry
Domain: Health Sciences
A Parallel, Four Degree-of-Freedom Robotic Wrist

Abstract Kinematic considerations are presented for a parallel, four degree-of-freedom robot wrist resembling the Clemens coupling, a constant-velocity joint first described in his 1872 patent. In its new form as a wrist, this device provides general orientational mobility as well as axial displacement through a plunge motion. A possibly more important hybrid of this wrist is identified as an artificially constrained, spherical, three degree-of-freedom pitchyaw-roll wrist that can easily be derived from this new concept. Because of its parallel architecture, the new wrist design displays favorable attributes including high strength-to-weight and stiffness-to-weight ratios, a large workspace, and an open center construction. Closed-form forward and inverse kinematics of the wrist are derived for both the three and four degree-of-freedom configurations, thereby making it a likely candidate for real-time control. Workspace plots are also presented that demonstrate the dexterity of the proposed wrist.

Topic: Mechanics and Biomechanics Studies
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
The Navy's Shipboard Waste Management Research &amp; Development Program

ABSTRACT Increasing federal regulatory restrictions on overboard waste discharge in national and international waters require that the Navy develop shipboard equipment and procedures to process and store a wide range of wastes onboard surface ships or, where permitted, to discharge certain wastes in environmentally acceptable forms. Navy policy and guidance recognizes the fleet's environmental responsibilities, and major research, development, test, and evaluation efforts are being conducted to develop and evaluate suitable shipboard waste processing systems for oily wastes, non‐oily wastewater, hazardous wastes/materials, and solid wastes. Environmental protection systems for back‐fit and forward‐fit are being developed. A wide range of shipboard requirements must be accommodated, including space, size/weight, safety/health, and reliability. Current priorities focus on plastics and other solid wastes, oily wastes, ozone depleting chlorofluorocarbons and blackwater. Significant progress is being made, and the Navy is confident that ship designs for the 21st century will be environmentally sound.

Topic: Maritime Transport Emissions and Efficiency
Subfield: Environmental Engineering
Field: Environmental Science
Domain: Physical Sciences
Pyogenic Liver Abscess in Normal Children With Fever of Unknown Origin

Solitary pyogenic hepatic abscesses were identified as the cause of fever, abdominal pain, and hepatomegaly in two otherwise normal children who were seen at St. Louis Children's Hospital during the past year. Liver function tests were normal and blood cultures were negative in both patients. These cases illustrate that pyogenic liver abscess may occur in normal children and should be considered whenever fever of unknown origin is associated with abdominal complaints. Only in this way can we hope to improve upon the results cited previously, namely that the majority of liver abscesses remain undiagnosed during life.

Topic: Amoebic Infections and Treatments
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences