jimnoneill/paper-to-field-training huggingface dataset:
Comparative Evaluation of the Accuracy ofImmunoassay with Liquid ChromatographyTandem Mass Spectrometry (LC/MS/MS) of UrineDrug Testing (UDT) Opioids and Illicit Drugs inChronic Pain Patients

Field: Medicine (Health Sciences)

Background: The challenge for physicians in treating chronic pain with opioids is to eliminate or significantly curtail abuse of controlled prescription drugs while assuring proper treatment when indicated. Urine drug testing (UDT) has been shown to be a useful approach in identifying patterns of compliance, misuse, and abuse. However, significant controversy surrounds the diagnostic accuracy of UDT performed in the office (immunoassay) and the requirement for laboratory confirmation with liquid chromatography tandem mass spectrometry (LC/MS/MS). Study Design: A diagnostic accuracy study of urine drug testing. Study Setting: The study was performed in an interventional pain management practice, a tertiary referral center, in the United States. Objective: The objective of this study was to compare the results of UDT of immunoassay inoffice testing (index test) to LC/MS/MS (reference test). Methods: One-thousand participants were recruited from an interventional pain management program. Urine sample was collected from all the consecutive patients with demographic information. Immunoassay testing was performed by a nurse at the location, laboratory assessment was performed with LC/MS/MS. Results of the index test were compared to the reference test in all patients. The sensitivity, specificity, false-positive, and false-negative rates, and index test efficiency (agreement) were calculated. Results: Overall, results showed that confirmation was required in 32.9% of the specimens. Agreement for prescribed opioids was high with the index test (80.4%). The reference test of opioids improved the accuracy by 8.9% from 80.4% to 89.3%. Non-prescribed opioids were used by 5.3% of patients. The index test provided false-positive results for non-opioid use in 44% or 83 of 120 patients. For illicit drugs, the false-positive rate by index test was 0% for cocaine, whereas it was 2% for marijuana, 0.9% for amphetamines, and 1.2% for methamphetamines. Limitations: The limitations include a single site study utilizing a single POC kit and a single laboratory, as well as technical sponsorship. Conclusion: The UDT with immunoassay in an office setting is appropriate, convenient, and cost-effective. Compared with laboratory testing for opioids and illicit drugs, immunoassay inoffice testing had high specificity and agreement, demonstrating the value of immunoassay drug testing. Because of variable sensitivity, clinicians would be well-advised to take a cautious approach when interpreting the results. Key words: Controlled substances, opioids, illicit drugs, abuse, liquid chromatography tandem mass spectrometry, immunoassay, urine drug testing
Bimodal age-frequency distribution of epitheliosis in cancer mastectomies relevance to preneoplasia

Field: Medicine (Health Sciences)

A census of epitheliosis in 500 consecutive cancer mastectomies has been carried out. The probability of concurrence of this phenomenon with cancer has a bimodal age-frequency distribution. It is high in cancer mastectomies from women in their early 40s, low in the late 50s and high again in the elderly. Epitheliosis during the reproductive life span is regarded as a reversible ovary-dependent abnormality. It is greatly increased in the premenopausal cancerous breast and it is thought that it carries increased risk for cancer initiation. In contrast the probability of epitheliosis in the breast in the elderly cancer patient is only slightly greater than in "noncancerous" post mortem breasts of similar age. Much of this "epitheliosis" may represent, in fact, indolent autonomous cancer though a small proportion could be epitheliosis supported by extraovarian estrogen.
Engineered autologous nasal cartilage for repair of nasal septal perforations: a case series

Field: Medicine (Health Sciences)

Objective: This phase I clinical trial assessed the use of autologous nasal chondrocyte tissue-engineered cartilage (N-TEC) for functional repair of nasal septal perforations (NSP). Background: The most widely used technique to treat NSP, namely interposition grafting with a polydioxanone (PDS) plate combined with a deep temporal fascia (DTF) graft, is still suboptimal towards patient satisfaction and revision rates. Methods: Patients ( n =5, all female, age range: 23–54 years) had a 0.5–2.0 cm diameter NSP. N-TEC was manufactured by expansion and 3D culture of autologous nasal septum chondrocytes into Chondro-Gide collagen membranes. N-TEC was then shaped intraoperatively and enveloped in the harvested DTF before suturing it into the NSP. Safety (primary outcome) was assessed by the number of serious adverse reactions (SAR) until 12 months. Secondary outcomes included feasibility, assessed by surgical graft manipulation, and efficacy, assessed using subjective scoring (nasal obstruction symptom evaluation, NOSE, and visual analog scale, VAS, scores) and objective breathing function tests. Structural closure of NSP after 12 months was defined using endoscopy and computed tomography (CT) scans. Results: NSP treatment by N-TEC implantation was safe and feasible, as no SAR and no challenge in graft manipulation was recorded for any of the patients. One year postoperative, subjective scoring improved in all patients, unless already optimal (average improvement of 23 and 28.6 points out of 100, respectively, for NOSE and VAS scores). Objective respiratory function overall confirmed – with the exception of one case – the observations above (average improvement of 172 ml/s). NSP were closed and the mucosae completely healed in three patients. Conclusion: Autologous N-TEC is a valid treatment for NSP and warrants further clinical tests.
PENALTY FUNCTION METHOD FOR MODELING OF CYLINDER FLOW WITH SUBSONIC COMPRESSIBLE FLOW

Field: Engineering (Physical Sciences)

Numerical modelling of compressible flows around moving solids is important for engineering applications such as aerodynamic flutter, rocket engines and landing gear. The penalty function method is particularly effective when using orthogonal structural meshes within a finite difference scheme and is widely used to solve both laminar and turbulent flow problems. The method is based on the direct application of the Navier-Stokes equations with added sources, which allows the boundary conditions to be set indirectly. This method facilitates the imposition of Dirichlet boundary conditions but complicates the application of Neumann conditions. Nevertheless, the method works well with both types of boundary conditions, making it suitable for thermal and compressible flows where Neumann conditions are often used. Despite its flexibility, the method requires a high degree of data management and additional coding. This paper presents results of a recently developed higher-order method for compressible subsonic flows, demonstrating accurate modeling of moving objects without numerical noise. The method has been tested on stationary and moving objects over a wide range of Reynolds and Mach numbers.
DEMENTIAS- ORIGINAL ARTICLE Association of the RAGE G82S polymorphism with Alzheimer’s disease

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

Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract The receptor for advanced glycation endproducts (RAGE) has been implicated in several pathophysiological processes relevant to Alzheimer’s disease (AD), including transport and synaptotoxicity of ADassociated amyloid b (Ab) peptides. A recent Chinese study (Li et al. in J Neural Transm 117:97–104, 2010) suggested an association between the 82S allele of the functional single nucleotide polymorphism (SNP) G82S (rs2070600) in the RAGE-encoding gene AGER and risk of AD. The present study aimed to investigate associations between AGER, AD diagnosis, cognitive scores and cerebrospinal fluid AD biomarkers in a European cohort of 316 neurochemically verified AD cases and 579 controls. Aside from G82S, three additional tag SNPs were analyzed to cover the common genetic variation in AGER. The 82S allele was associated with increased risk of AD (Pc = 0.04, OR = 2.0, 95 % CI 1.2–3.4). There was no genetic interaction between AGER 82S and APOE e4 in producing increased risk of AD (P = 0.4), and none of the AGER SNPs showed association with Ab42, T-tau, P-tau181 or mini-mental state examination scores. The data speak for a weak, but significant effect of AGER on risk of AD.
The appropriateness and fulfilment of rehabilitative parole conditions imposed by district prisons boards

Field: Social Sciences (Social Sciences)

The present study reviews some aspects of the New Zealand District Prisons Boards parole system, as governed by the Criminal Justice Act (1985). The Boards of Papaura and Rolleston are presented as examples. Of those granted parole by the Boards from May 1990 to September 1990, (N=39), psychological assessment provided incidence figures of drug and alcohol disorders (Diagnostic anger interview schedule), and anger problems (State Trait Anger Expression Inventory; and offenders classifying themselves as Maori (Cultural inventory devised for present study). Degree of matchin of problems to special parole conditions was determined by chi-square and phi-coefficient, along with the proportion of hits and correct rejections, to false alarms and misses. Statistically, a satisfactory match had occurred in drug, alcohol, and Maoritanga. Anger indicated a very poor match. Fulfilment of special conditions indicated that at 10 weeks, 8% had fulfilled all special parole conditions; 34% had fulfilled all mandatory conditions; and 50% fulfilled one condition; while no parolee fulfilled more than one condition. At six months after release, 27% of parolees had been reconvicted, with one being reincarcerated. Recommendations are made, regarding ways in which the Justice Department might address problems highlighted in the present research, including issues pertaining to the incorporation of actuarial prediction techniques in parole selection.
Fossil leaves of Banksia, Banksieae and pretenders: resolving the fossil genus Banksieaephyllum

Field: Earth and Planetary Sciences (Physical Sciences)

The genus Banksieaephyllum, originally erected for cuticle-bearing fossil leaves of subtribe Banksiinae (Proteaceae subfamily Grevilleoideae, tribe Banksieae), is reassessed. Of the 18 described species, nine are accepted within Banksia, including Banksieaephyllum obovatum Cookson & Duigan, which is synonymised with B. laeve Cookson & Duigan on the basis of new cuticular preparations. Two other species are transferred to Banksieaefolia gen. nov., a genus erected for Banksieae of uncertain affinities, and which presently includes only fossils that probably belong to subtribe Musgraveinae. The seven other Banksieaephyllum species lack definitive characters of Proteaceae (i.e. brachyparacytic stomata and annular trichome bases) and do not have Banksieae-type cylindrical trichome bases. These species are, therefore, not accepted as Proteaceae and are transferred to Pseudobanksia gen. nov., together with another fossil Banksia-like leaf species, Phyllites yallournensis Cookson & Duigan. Lectotypes are chosen for Banksia fastigata H.Deane, Banksieaephyllum acuminatum Cookson & Duigan, Banksieaephyllum angustum Cookson & Duigan and Banksieaephyllum laeve Cookson & Duigan. Implications arising from the re-assessment of Banksieaephyllum include clarification of biome conservatism in Banksieae; Banksia has long had an association with relatively open, sclerophyllous vegetation, and Musgraveinae with rainforest. Pseudobanksia and Banksia share convergent traits, but in contrast to Banksia, Pseudobanksia failed to survive the drying climates and increased fire-frequencies of the Neogene.
Global dynamics of some systems of higher-order rational difference equations

Field: Mathematics (Physical Sciences)

Abstract In the present work, we study the qualitative behavior of two systems of higher-order rational difference equations. More precisely, we study the local asymptotic stability, instability, global asymptotic stability of equilibrium points and rate of convergence of positive solutions of these systems. Our results considerably extend and improve some recent results in the literature. Some numerical examples are given to verify our theoretical results. MSC: 39A10, 40A05.
Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools

Field: Computer Science (Physical Sciences)

Proteins are the workhorses of life and gaining insight on their functions is of paramount importance for applications such as drug design. However, the experimental validation of functions of proteins is highly-resource consuming. Therefore, recently, automated protein function prediction (AFP) using machine learning has gained significant interest. Many of these AFP tools are based on supervised learning models trained using existing gold-standard functional annotations, which are known to be incomplete. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, due to the incompleteness of gold-standard data, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the \emph{oracle problem}. In this work, we use metamorphic testing (MT) to test nine state-of-the-art AFP tools by defining a set of metamorphic relations (MRs) that apply input transformations to protein sequences. According to our results, we observe that several AFP tools fail all the test cases causing concerns over the quality of their predictions.
FPGA Accelerated HPC and Data Analytics

Field: Computer Science (Physical Sciences)

Summary form only given, as follows. The complete presentation was not made available for publication as part of the conference proceedings. There are increasing opportunities in the data center for FPGA algorithm, networking, and data access acceleration. Microsoft has announced that they accelerate Bing search, machine learning, and networking with FPGAs - and they recently announced integration of FPGA based Project Brainwave with Azure Machine Learning for real-time AI. FPGAs also deliver some future-proofing for AI, with current support for reduced precision floating point and bfloat16 for better performance with minor loss of scoring accuracy. Intel and partners are also integrating FPGAs to data analytics frameworks and existing databases to enable enterprise customers to run unmodified applications without requiring any FPGA expertise for use with unstructured, NoSQL, and traditional relational databases. One such partner, Swarm64, is using a single FPGA for multiple acceleration roles to deliver 2X+ performance on the industry standard TPC-H benchmark.
Dendroclimatology in Latin America: A Review of the State of the Art

Field: Earth and Planetary Sciences (Physical Sciences)

The application of dendrochronology for understanding climatic variations has been of great interest to climatologists, ecologists, geographers, archeologists, among other sciences, particularly in recent decades when more dendrochronological studies have been developed. We analyzed and identified the current state and recent advances in dendroclimatology in Latin America for the period 1990 to 2020. We carried out reviews in ScienceDirect, Web of Science, and Scopus databases with the keywords “dendrochronology”, “dendroclimatology”, “dendrochronology and climatic variability”, “dendroclimatology and climatic variability”, “dendrochronology and trend”, and “dendroclimatology and trend” for each Latin American country. Results show that dendroclimatological research in the last 11 years has increased and has been mainly developed in temperate climate zones (83%) and tropical or subtropical areas (17%), where conifer species have been the most used with over 59% of the studies. However, broadleaf species for dendrochronological studies have also increased in the last decade. Dendroclimatological research in Latin America has provided important advances in the study of climatic variability by defining the response functions of tree-rings to climate and developing climatic reconstructions. Our research identified areas where it is necessary to increase dendroclimatic studies (e.g., dry and tropical forests), in addition to applying new techniques such as isotope analysis, blue intensity, dendrochemistry, among other tree-ring applications.
Develop an APP for quantitative detection of alpha fetoprotein

Field: Health Professions (Health Sciences)

Alpha fetoprotein (AFP) is an important biomarker for the early detection and effective therapy of cancer. Existing technologies for AFP detection, however, have significant limitations, such as complex processes, lengthy detection cycles, and high costs, which limit their practical usage in clinical settings. To address these issues, this project intends to provide an innovative and disruptive solution in the form of a dedicated mobile application (APP).This APP promises to change AFP detection paradigms by leveraging unique intellectual property containing AFP specific binding affinity peptides. By using these peptides, the proposed mobile application aims to overcome the limitations of previous approaches. This APP aims to ease the process of quantifying AFP levels using a user-friendly interface. The program aims to streamline detection methods by strategically combining cutting-edge technology with proprietary peptides, lowering complications and detection time.Furthermore, the use of privately held intellectual property might result in cost reductions during the APP's development and deployment phases. This strategic approach lays the groundwork for a more cost-effective and financially feasible solution. In essence, the suggested mobile application not only promises to improve AFP detection precision and efficiency, but it also has the ability to transform the landscape of cancer diagnostics in a more accessible and impactful way.
Intraoperative electrophysiology during single-level selective dorsal rhizotomy: technique, stimulation threshold, and response data in a series of 145 patients

Field: Neuroscience (Life Sciences)

OBJECTIVE Selective dorsal rhizotomy (SDR) is effective at permanently reducing spasticity in children with spastic cerebral palsy. The value of intraoperative neurophysiological monitoring in this procedure remains controversial, and its robustness has been questioned. This study describes the authors’ institutional electrophysiological technique (based on the technique of Park et al.), intraoperative findings, robustness, value to the procedure, and occurrence of new motor or sphincter deficits. METHODS The authors analyzed electrophysiological data of all children who underwent SDR at their center between September 2013 and February 2019. All patients underwent bilateral SDR through a single-level laminotomy at the conus and with transection of about 60% of the L2–S2 afferent rootlets (guided by intraoperative electrophysiology) and about 50% of L1 afferent roots (nonselectively). RESULTS One hundred forty-five patients underwent SDR (64% male, mean age 6 years and 7 months, range 2 years and 9 months to 14 years and 10 months). Dorsal roots were distinguished from ventral roots anatomically and electrophysiologically, by assessing responses on free-running electromyography (EMG) and determining stimulation thresholds (≥ 0.2 mA in all dorsal rootlets). Root level was determined anatomically and electrophysiologically by assessing electromyographic response to stimulation. Median stimulation threshold was lower in sacral compared to lumbar roots (p < 0.001), and 16% higher on the first operated (right) side (p = 0.023), but unrelated to age, sex, or functional status. Similarly, responses to tetanic stimulation were consistent: 87% were graded 3+ or 4+, with similar distributions between sides. This was also unrelated to age, sex, and functional status. The L2–S2 rootlets were divided (median 60%, range 50%–67%), guided by response to tetanic stimulation at threshold amplitude. No new motor or sphincter deficits were observed, suggesting sparing of ventral roots and sphincteric innervation, respectively. CONCLUSIONS This electrophysiological technique appears robust and reproducible, allowing reliable identification of afferent nerve roots, definition of root levels, and guidance for rootlet division. Only a direct comparative study will establish whether intraoperative electrophysiology during SDR minimizes risk of new motor or sphincter worsening and/or maximizes functional outcome.
Shaping Cash Transfer Impacts Through ‘Soft-Conditions’: Evidence from Lesotho†

Field: Economics, Econometrics and Finance (Social Sciences)

Cash transfer programmes have been shown to have positive effects on a variety of outcomes. While much of the literature focuses on the role of conditionality in achieving desired impact, this paper focuses on the role of ‘soft conditionality’ implemented through both ‘labelling’ and ‘messaging’ in evaluating the impact of the Child Grants Program in Lesotho, an unconditional cash transfer programme targeting poor households with orphans and vulnerable children. Beneficiary households received a clear message that the transfer should be spent on the interest and needs of children. Our \nfindings suggest that ‘soft conditionality’ does play a role in increasing expenditure for children, especially on education, clothing and footwear. Results indicate in fact that transfer income is spent differently from general income as it exerts both an income and a substitution effect. This behavioural change is confirmed by comparing the ex-ante expected behaviours with the ex-post actual response to the programme. We find that for expenditure categories linked to the well-being of children the expost response was much higher than the ex-ante expected behaviour.
Effect of Salinity on Germination and Seed Physiology in Bean (Phaseolus Vulgaris L.)

Field: Agricultural and Biological Sciences (Life Sciences)

The response of three bean cultivars (Phaseolus vulgaris L.) to equimolar NaCl and Na2SO4 salinity at germination and early seedling growth was investigated. Seeds were germinated and grown in Petri plate on filter paper with solution of the respective treatment and incubated at 25°C in a thermostat. Each treatment was replicated three times. The seedlings were harvested and their growth, as well as their germination and respiration rates were measured.All treated cultivars registered decrease in the percentage of germination, seedlings growth and respiration rate. The cultivars were inhibited stronger by Na2SO4 than NaCl treatment.
Revisiting the Synod of Dordt (1618–1619). Edited by Aza Goudriaan and Fred van Lieburg. (Brill's Series in Church History, 49.) Pp. xiv+442 incl. 13 ills. Leiden–Boston: Brill, 2011. €99. 978 90 04 18863 1; 1572 4107

Field: Arts and Humanities (Social Sciences)

Revisiting the Synod of Dordt (1618–1619). Edited by Aza Goudriaan and Fred van Lieburg. (Brill's Series in Church History, 49.) Pp. xiv+442 incl. 13 ills. Leiden–Boston: Brill, 2011. €99. 978 90 04 18863 1; 1572 4107 - Volume 63 Issue 2