jimnoneill/paper-to-field-training huggingface dataset:
Local transition gradients determine the global attributes of protein energy landscapes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational changes. Unfortunately, the relationship between local atomic fluctuations and global protein rearrangements is still elusive. Here, atomistic molecular dynamics simulations in conjunction with complex network analysis show that fast peptide relaxations effectively build the backbone of the global free-energy landscape, providing a connection between local and global atomic rearrangements. A minimum-spanning-tree representation, built on the base of transition gradients networks, results in a high resolution mapping of the system dynamics and thermodynamics without requiring any a priori knowledge of the relevant degrees of freedom. These results suggest the presence of a local mechanism for the high communication efficiency generally observed in complex systems.
BetaBeat Blood Sugar Support

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

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Residential Mobility, Family Structure, and the Cell-Only Population

Field: Social Sciences (Social Sciences)

The cell-phone-only (CPO) population has grown rapidly over the past several years, causing concern for researchers who rely mostly on random digit dialing (RDD) of landlines to conduct their research. While early research on CPOs has focused largely on age differences, CPOs may differ from those with landlines in many other ways even after controlling for age. In this article, we use the Cooperative Congressional Election Study-an Internet survey based on matched random sampling-and the American National Election Study-an in-person survey based on stratified residential sampling-to examine the potential effects of the cell-only population for survey research. These surveys are ideal for studying the causes and consequences of cell-only lifestyles for survey research because they reach cell-only and landline respondents through a single sampling frame. We reach two main conclusions: (1) CPO households are not simply a function of age, but of other factors as well, especially residential mobility and family structure; and (2) there are notable differentials in vote preferences and turnout between CPOs and others.
Figure S4 from CREBBP/EP300 Bromodomain Inhibition Affects the Proliferation of AR-Positive Breast Cancer Cell Lines

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

<p>Effects of treatments on MYC expression. mRNA determined by qPCR and normalized to GAPDH expression (top panel) and protein levels determined by western blot (bottom panel) of MYC after treatment of cells with 2 μM CBP30, 10 μM C646 and 150 nM JQ1 for 48 hours.</p>
Characterization of the Metabolism, Distribution and Toxicity of 2,6-di-t-Butyl-4-Nitrophenol for Purposes of Health Hazard Assessment

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Abstract : In 1992, the Navy Environmental Health Center, Norfolk, VA was made aware of the concern about the discoloration (yellowing) of interiors (e.g. bulkheads and bedding) and the possible exposure of navy personnel aboard submarines, to an - unknown substance. The agent was identified as 2,6-di-tert-butyl-4-nitrophenol (DBNP). The yellowing process appeared to arise from the reaction of 2,6-di-tert-butylphenol (DBP), an antioxidant additive used in engine lubricant, with NO2 in the submarine atmosphere. A research program was initiated for health hazard assessment of DBNP. - This technical report summarizes the results of our research program and the information available in the literature.
Culture, consciousness and armed conflict: Cabral's déclassé/(lumpenproletariat?) in the era of globalization*

Field: Social Sciences (Social Sciences)

This paper compares critically Cabral and Frantz Fanon's readings of class struggle in Africa. Class definitions imported from Marxism had a different utilization by Cabral, more close to a pragmatic interpretation based on the groundroots experience. The divergence between Cabral and Fanon's interpretations can be projected to current debates to demonstrate these are still unresolved issues amongst most African scholars when assessing other revolutionary experiments in the continent.
Punishing assault: the transformation of attitudes in the English courts

Field: Social Sciences (Social Sciences)

In early modern England physical violence was regarded as an acceptable instrument of social policy and of individual and group interaction by almost all sectors of society. There were dissenting voices and differences of emphasis, but violence was accepted as the primary means by which the state punished offenders. It was also an intrinsic part of many popular recreations, and was usually seen as a legitimate way to resolve interpersonal disputes. This atmosphere of acceptance changed rapidly, if by no means uniformly, in the late eighteenth and early nineteenth centuries, but research on this vital transition has been confined largely to the first two of these three dimensions.
The role of growth factors in extraction wound healing

Field: Dentistry (Health Sciences)

Wound healing is a complex process that includes hemostasis, inflammation, proliferation and tissue remodeling. Growth factors are natural biological mediators that regulate crucial cellular processes involved in the tissue repair, such as DNA synthesis, angiogenesis, metabolic activity, migration, chemotaxis, proliferation, differentiation and matrix synthesis. The most important growth factors that play a part in the extraction-wound healing process and bone tissue regeneration are: platelet - derived growth factor-PDGF, transforming growth factor Beta-TGF β, insulin-like growth factor-lGF, bone morfogenetic protein-BMP-2, BMP- 7 ,vascular endothelial growth factor- VEGF, fibroblast growth factor-FGF. Growth factors appear at various concentrations at different times, so that the wound age may be estimated by their age. Except wound healing growth factors may be used in better oseointegration of imlants, alveolar ridge augmentation, alveolit etc. Studies of physiological processes in which growth factors have a regulatory role indicate that these molecules rarely act in biological isolation. The study of the interaction between the growth factors in the alveolar bone can explain tissue ability to heal even under adverse conditions, such as infection and radiation.
IBM POWER6 accelerators: VMX and DFU

Field: Computer Science (Physical Sciences)

The IBM POWER6™ microprocessor core includes two accelerators for increasing performance of specific workloads. The vector multimedia extension (VMX) provides a vector acceleration of graphic and scientific workloads. It provides single instructions that work on multiple data elements. The instructions separate a 128-bit vector into different components that are operated on concurrently. The decimal floating-point unit (DFU) provides acceleration of commercial workloads, more specifically, financial transactions. It provides a new number system that performs implicit rounding to decimal radix points, a feature essential to monetary transactions. The IBM POWER™ processor instruction set is substantially expanded with the addition of these two accelerators. The VMX architecture contains 176 instructions, while the DFU architecture adds 54 instructions to the base architecture. The IEEE 754R Binary Floating-Point Arithmetic Standard defines decimal floating-point formats, and the POWER6 processor—on which a substantial amount of area has been devoted to increasing performance of both scientific and commercial workloads—is the first commercial hardware implementation of this format.
Comparison of Using Different Types of Wavelet or FFT for De-nosing of Body Surface Potential Signals

Field: Computer Science (Physical Sciences)

Body surface potential mapping (BSPM) is a non-invasive functional imaging method for reconstructing electrophysiological information about the surface of the heart. BSPM provides more diagnostic information than the 12-lead ECG. De-noising body surface potential (BSP) signals would lead to more accurate BSPM patterns therefore better diagnosis for heart problems. For de-noising of body surface potential signals we used FFT and also different types of wavelets as a de-nosing tool and compare their results with the help of a quantitative value called Signal Error Ratio (SER). Wavelets show better results in compare to FFT. After de-noising all of the BSP signals, changes in BSPM patterns are also presented to show the effects of our method in de-noising BSPs.
Treatment compliance in patients with metastatic renal cell carcinoma.

Field: Medicine (Health Sciences)

e16560 Background: Treatment for metastatic renal cell carcinoma (mRCC) includes surgery, immunotherapy, and/or targeted therapy: kinase inhibitors (including mTOR) and anti-VEGF agents. Little is known about real-world compliance to these emerging treatments. This analysis utilizes recent data to provide insight into compliance, an important component of effectiveness. Methods: A retrospective observational study using SDI Health's claims data was conducted. The study period encompassed 1/1/2005 to 9/30/2009. Qualifying patients were adults diagnosed with RCC, and then diagnosed with a secondary neoplasm (n = 179) or treated with IL-2, IFN, sunitinib, sorafenib, temsirolimus, everolimus or bevacizumab (n = 470) during the study period. A 90-day gap in therapy defined the start and end of therapy. Compliance was measured as the medication possession ratio (MPR). For oral therapies, the MPR was calculated as (the number of days of supply dispensed/the number of days the patient was on therapy). For infused therapies, the MPR was defined as (the administration day plus the duration of clinical benefit (DCB)/the number of days the patient was on therapy). The DCB was based on the recommended frequency of administration in the label and regimen guidelines. Results: The study sample of 649 newly treated mRCC patients had a median age of 63 years. Male patients were more than double females (68.1 vs. 31.9%). Patients were generally very compliant across the entire range of mRCC regimens; the majority (i.e., 86.5% of patients) had an MPR ≥ 80%: the literature's threshold for high compliance. First line and second line patients had similar compliance (mean MPR 91.8% vs. 89.3%, p = 0.34). Within first line, oral therapy had a statistically higher MPR than infused therapy (0.94 vs. 0.89, p < 0.0001) but no difference was observed in second line (0.91 vs. 0.87, p=0.19). Conclusions: The observed compliance was similar across all treatment regimens and administration routes (oral vs. IV) for mRCC patients. Similar rates of compliance likely reflect varying combinations of contributing factors including safety, efficacy, and access to therapy. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Novartis Novartis Novartis Novartis
Prognostic impact of bone involvement in Hodgkin lymphoma.

Field: Medicine (Health Sciences)

The purpose of the study is to determine incidence and prognostic impact of osseous Hodgkin lymphoma (HL). Between 1997 and 2004, 198 patients with HL were treated at our institution. Advanced stages and nodular sclerosis histology prevailed. All patients were treated according to protocols of the German Hodgkin Study Group (GHSG). After minimum follow-up of 24 months, we retrospectively analyzed the incidence of osseous HL, treatment response and parameters of survival. We recorded 14 cases of osseous HL (7 %), always with concurrent nodal disease. Axial skeleton was most frequently involved. Eleven patients (78,5 %) achieved complete remission and three (21,5 %) progressed primarily. The patients with osseous HL had significantly lower 2-year freedom from treatment failure than the patients without bone involvement (71,4 and 92,7 %, respectively, p=0,004), with no significant difference in 2-year overall survival (85,7 and 95 %, respectively, p=0,14). On multivariate analysis, advanced stage was the only independent adverse prognostic factor. In conclusion, bone involvement is a relatively common finding in HL and is not an independent adverse prognostic factor.
Spectral Plain: A case study for exploring the world-building potential of co-creative systems that combine text generation models with game mechanics

Field: Computer Science (Physical Sciences)

SHORT PAPER. This paper describes the game installation ‘Spectral Plain’; introducing a case study of an interactive artwork that intersects algorithmic, sensing, and gaming technologies to explore new forms of generative world-building, which are different from the world-imaginations created by commercial and political narratives. Through this case study, we aim to explore how information technologies might embed specific socio-cultural beliefs. Here, we investigate the imaginaries created and disseminated through dominant representations of information technologies, while simultaneously searching for ways to create new multiscalar imaginaries of the earth through the mobilisation of these technologies. This case study describes how physical and digital interactions can be combined with AI and randomising technologies to foster forms of co-creation with and between humans. It also explores the capacity for AI-integrated game environments to decenter anthropogenic perspectives by creating new symbiotic interrelations with the non-human and the non-living that can impact participants’ perception of their understanding of the world.
Ordering Process in CuPd Alloys during Continuous Heating

Field: Materials Science (Physical Sciences)

The ordering process during continuous heating in Cu-Pd alloys containing 34.74∼44.80 at%Pd was investigated by means of electrical resistivity measurements, X-ray diffraction, hardness test and transmission electron microscopy.In all alloys, the electrical resistivity increased slightly in the early stage of ordering. This increase in resistivity was found to be due to the development of short range order in the disordered α phase. The activation energy for this stage was evaluated to be 83.7∼100.4 kJ/mol, being equal to the migration energy of quenched-in vacancies in α phase.In alloys whose compositions are in the two phase region of (α1+β), ordering occurred through two processes (viz. stage I and II). In the stage I, the electrical resistivity decreased slightly and microdomains of short range order grew markedly. It is suggested that the vacancy-hydrogen atom complexes dissociate into a vacancy and a hydrogen atom in the stage I, and newly produced vacancies contribute to the marked growth of microdomains of short range order.The hardening of the alloy was attained by the increase in volume fraction of the ordered β phase. The hardness of β phase decreased gradually with the growth of anti-phase domain size.
Multiphoton absorption of OsO_4 under two-CO_2-laser pulse excitation

Field: Chemistry (Physical Sciences)

Measurements of multiphoton absorption from the second nonresonant laser beam under two-frequency infrared-laser excitation of OsO4 are reported. Dissociation energy, the fraction of molecules excited by the first resonant laser pulse, and the excitation level have been estimated on the basis of these measurements. The kinetics of highly vibrationally excited molecules is discussed.
Response of Maize (Zea mays L.) to Poultry Dung Compost on Sandy Soil in Toumodi, Central Côte d'Ivoire

Field: Agricultural and Biological Sciences (Life Sciences)

The increase in maize harvests among farmers in the Toumodi locality (6°25'4.8˝N and 5°4'19.2˝w), in Côte d'Ivoire, required a study during the June cropping season in 2023. 4 increasing doses of compost: T0 (0 t/ha), T1 (10 t/ha), T2 (15 t/ha) and T3 (20 t/ha), were applied to the soil (0 - 20 cm) in a Fischer-type set-up with 4 replications. The mean values of the yield components of the various treatments were compared with each other and with those of the blank control using analyses of variance for a critical threshold, α = 0.05. Flowering was observed in male and female plants after 50 days following sowing in all the amended plots, whereas it appeared 10 to 15 days later in the plots without application. The highest grain yields were noted in the plots receiving the 15 t/ha dose, with average harvests of around 5 t/ha compared with 1.9 t/ha for the treatment without application. In addition, the 15 t/ha dose produced more seeds than the other treatments. In addition to its availability, the compost tested is rich in nutrients. An application of at least 10 t/ha is enough to increase yields, which are estimated to be almost twice as high as those in soils without compost. To this end, spreading this material on farmers' fields is highly desirable. However, the use of compost requires pre-treatment of the raw organic material, which could be a constraint on its use.
Amplifying the learning effects via a Forecasting and Foresight Support System

Field: Business, Management and Accounting (Social Sciences)

Nowadays, informed decision making is conducted through innovative Information and Communication Technology (ICT) support systems. In order to utilize such ICT-based support systems fully, decision makers need suitable training. This paper proposes and evaluates the use of a Forecasting and Foresight Support System in an undergraduate course in business forecasting, so as to amplify the learning effect. The system provides a simple implementation of the forecasting process via realistic business scenarios that utilize both quantitative and qualitative information. Classical operational forecasting related features, as well as elements of a foresight nature, are considered during an exercise, so as to enhance user experience in terms of collaboration and communication. The system’s acceptance and perceived educational effects are determined through responses to a purpose-built questionnaire. The results are very encouraging in terms of the final amplification of the learning effect.
The Age of Athanasius

Field: Arts and Humanities (Social Sciences)

The publication of the Fourth Report of the Ritual Commission in 1870 occasioned intense debate over the position of the Athanasian Creed in the liturgy of the Church of England. This article reconstructs the course of that controversy, focusing particularly on the centrality of historical argument to the speeches, letters, and pamphlets in which critics and defenders of the formulary sought to stabilise Christian orthodoxy and define Anglican identity in a progressive environment. The episode draws attention, first, to the continuing and underestimated centrality of patristic scholarship to questions of church reform in Victorian England, whilst also pointing towards the eventual decline of the textual and antiquarian approach to apologetics that had characterised Anglicanism since the Reformation. Post-Reformation Anglican history, secondly, was itself integral to participants’ articulation of religious division, suggesting that conventional understandings of “church parties” in the Victorian Church of England should accordingly be revised.
Influence of Cadophora finlandica and other microbial treatments on cadmium and zinc uptake in willows grown on polluted soil

Field: Environmental Science (Physical Sciences)

We conducted a pot experiment to evaluate the Cd and Zn accumulation in leaves and roots of Salix smithiana (BOKU-03DE-001) and S. caprea (BOKU-01AT-004) clones grown on a metal-contaminated soil as affected by native microbes extracted from the same experimental soil, and the fungus Cadophora finlandica. Plant biomass production of S. smithiana was decreased in all the treatments compared to the sterilized control. In contrast, S. caprea grew best on the non-sterilized soil. Similar effects were observed for plant Zn and Cd contents. Microbial treatments affected metal accumulation differently in the two Salix species. The effects of the microbial treatments on biomass and metal content of leaves were not related to the degree of mycorrhization. A comparison with literature data suggests that the plant response to microbial inoculation in terms of metal accumulation may depend on the plant-internal metal concentration. Our findings also illustrate a difficulty of successful rhizosphere management using metal-tolerant microbial isolates to further enhance the phytoextraction process.
Abstract 151: Software Annotation of Defibrillator Files: Ready for Prime Time?

Field: Medicine (Health Sciences)

Introduction: Defibrillators record important information about the quality of chest compressions during CPR. Software made for reviewing defibrillator files automatically annotate and measure chest compression metrics. However, evidence is limited regarding the accuracy of such measurements. Objective: To compare chest compression fraction (CCF) and rate measurements made with software annotation vs. manual annotation of defibrillator files. Methods: This is a retrospective, observational study from the Dallas Fort-Worth site of the Resuscitation Outcomes Consortium. We reviewed chest compression waveforms from the bioimpedance channel of defibrillator recordings (Physio-Control Lifepak 12 and 15, Redmond, WA) of 100 prehospital patients enrolled in the DFW Cardiac Arrest Registry from 9/8/2018 to 3/9/2019. Included cases were ≥18 years, had presumed cardiac cause of arrest, and continuous chest compressions. We assessed chest compression waveforms from the time of initial CPR until the time the defibrillator was removed. A trained reviewer revised the software annotations by marking the start and end of CPR and adding or removing chest compressions. Software annotated and manual reviewer annotated measurements were compared for CCF and rate using intraclass correlation coefficient (ICC) statistical analysis. Results: Mean patient age was 63 years with 59% male. The mean (±SD) duration of CPR was 30.4 ± 10.6 min. The overall mean CCF for files annotated by software vs. manual annotation was 0.64 ± 0.19 vs. 0.86 ± 0.07, respectively, and the ICC was 0.14. For software vs. manual annotation, the overall mean rate was 109 ± 10 vs. 108 ± 10, respectively, and ICC was 0.99. The software misidentified epochs before the start of chest compressions, failed to capture epochs after resuscitation ended, and after return of spontaneous circulation, resulting in low ICC for CCF. The ICC was excellent for compression rate because the software only counted epochs where chest compressions were actually given. Conclusions: Software annotation performed poorly for chest compression fraction and very well for chest compression rate. Defibrillator files must be reviewed and annotated manually before quality of chest compression measurements are calculated.