jimnoneill/paper-to-field-training huggingface dataset:
Detection of proteins and nucleic acids of Newcastle disease virus in<i>Eimeria acervulina</i>

Ten-day-old specific pathogen free (SPF) chickens were inoculated simultaneously with Eimeria acervulina and Newcastle disease virus (NDV). By employing immunofluorescent staining and in situ hybridization techniques, we detected NDV proteins and nucleic acids in different life stages of E. acervulina. However, no NDV particle was found within E. acervulina by electron microscopy. Oocysts from E. acervulina that contained NDV proteins and nucleic acids could elicit antibodies against NDV after repeated inoculation into SPF chickens. Moreover, the proportion of oocysts from chickens infected with E. acervulina and NDV which could be induced to sporulate in vitro was lower than those from chickens infected with E. acervulina alone. These results indicate that nucleic acids and proteins of NDV can exist within E. acervulina, and stimulate an immune response against NDV in chickens, and that NDV may also interfere with the sporulation of oocysts.

Topic: Coccidia and coccidiosis research
Subfield: Animal Science and Zoology
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Organic petrology and geochemistry data reveal depositional and thermal history of coal in the Guaduas formation, Colombian Eastern Cordillera

Colombia is a country rich in coal deposits; however, there are few published studies characterizing these coals in detail from a scientific perspective. This study investigates the thermal maturity and depositional environment of a coal seam from the Guaduas formation (Maastrichtian-Paleocene) of the Eastern Colombian Cordillera Basin, providing insight into burial and temperature history and changes in the depositional environment over time. This three-meter-thick hard coal seam reflects about 20 m of former peat deposition, representing a period of roughly 10.000 years. Five large, fresh samples (A to E) were collected from the seam every thirty centimeters and divided into seventeen sub-samples analyzed using organic petrological methods, Rock-Eval pyrolysis and organic geochemistry. Different thermal maturity- and depositional environment-related parameters have been determined. Results reveal a maturity of approximately 0.9% vitrinite reflectance, and relatively high HI values (kerogen type II-III). Correspondingly, high values of νCHx over γCH indicate a high relative abundance of aromatic rings over aliphatic groups. Moreover, high CH2/CH3 ratios suggest long and simple aliphatic chain structures. Molecular data indicate a balanced odd- over even n-alkane distribution and a high amount of long-chain n-alkanes. High Pr/Ph ratios and hopanoid biomarkers reveal an oxidizing depositional environment. The coal seam investigated in this study is characterized by low ash yields and low sulfur contents particularly in the central part of the seam, while percentages of inertinite are high (up to 54 Vol.-%). This data supports a low water table and oligotrophic, raised bog conditions during deposition in a humid, tropical climate which is consistent with the almost equatorial position of the study area during deposition of the Guaduas Formation. Water was mainly supplied via rainfall leading to overall low ash yields. In contrast, the top of the coal seam is strongly enriched in sulfur revealing that rapid marine flooding ultimately ceased peat accumulation leading to authigenic pyrite formation.

Topic: Geological and Tectonic Studies in Latin America
Subfield: Geophysics
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Application of the set pair analysis based on entropy and weight to efficiency evaluation of the BDAR for amphibious equipment

Aiming at the particularity of the BDAR, the method which employs the set pair analysis based on entropy and weight to rational efficiency evaluation of the BDAR had been discussed by taking certain five amphibian equipments as example. Firstly, the evaluating index system was established by analyzing the characteristic of the BDAR and the factors which affect the efficiency evaluation of the BDAR. Secondly, an evaluation model of the efficiency of the BDAR was built based on the set pair analysis and entropy weight, and its weight of evaluation indexes was gained by calculating the entropy in order to form the optimization matrix. Then the equipment which has the optimal efficiency of BDAR was chosen after the five candidates being ranked by comparing their degrees of identities. At last, the theory of the set pair analysis was validated, and scientific basis of the optimum and elevation of the equipment was proved.

Topic: Research studies in Vietnam
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Ultrasensitive detection of oncogenic human papillomavirus in oropharyngeal tissue swabs

Background The incidence of oropharyngeal squamous cell carcinoma (OPSCC) caused by oncogenic human papillomavirus (HPV) is rising worldwide. HPV-OPSCC is commonly diagnosed by RT-qPCR of HPV E6 and E7 oncoproteins or by p16 immunohistochemistry (IHC). Droplet digital PCR (ddPCR) has been recently reported as an ultra-sensitive and highly precise method of nucleic acid quantification for biomarker analysis. To validate the use of a minimally invasive assay for detection of oncogenic HPV based on oropharyngeal swabs using ddPCR. Secondary objectives were to compare the accuracy of ddPCR swabs to fresh tissue p16 IHC and RT-qPCR, and to compare the cost of ddPCR with p16 IHC. Methods We prospectively included patients with p16 + oral cavity/oropharyngeal cancer (OC/OPSCC), and two control groups: p16 − OC/OPSCC patients, and healthy controls undergoing tonsillectomy. All underwent an oropharyngeal swab with ddPCR for quantitative detection of E6 and E7 mRNA. Surgical specimens had p16 IHC performed. Agreement between ddPCR and p16 IHC was determined for patients with p16 positive and negative OC/OPSCC as well as for healthy control patients. The sensitivity and specificity of ddPCR of oropharyngeal swabs were calculated against p16 IHC for OPSCC. Results 122 patients were included: 36 patients with p16 + OPSCC, 16 patients with p16 − OPSCC, 4 patients with p16 + OCSCC, 41 patients with p16 − OCSCC, and 25 healthy controls. The sensitivity and specificity of ddPCR of oropharyngeal swabs against p16 IHC were 92 and 98% respectively, using 20–50 times less RNA than that required for conventional RT-qPCR. Overall agreement between ddPCR of tissue swabs and p16 of tumor tissue was high at κ = 0.826 [0.662-0.989]. Conclusion Oropharyngeal swabs analyzed by ddPCR is a quantitative, rapid, and effective method for minimally invasive oncogenic HPV detection. This assay represents the most sensitive and accurate mode of HPV detection in OPSCC without a tissue biopsy in the available literature.

Topic: Head and Neck Cancer Studies
Subfield: Otorhinolaryngology
Field: Medicine
Domain: Health Sciences
Mayer‐wave related oscillations (MWROs) are present in the vagal outflow during chemosensitive challenge

The central coordination of respiratory and vasomotor functions is likely to be modulated by a diffuse neural network, providing a common rhythmical background, based on the interaction between respiratory and Mayer wave-related rhythms. While MWROs have been recently described in the brainstem respiratory network (Morris et al., 2010), evidence of the presence of this rhythm in vagal outflow is still lacking. In a decerebrate cat preparation, arterial blood pressure (BP), cervical sympathetic and vagal outflows were recorded at baseline (B) and during two stimuli: the injection of CO2-satured saline via vertebral artery (central chemoreceptor stimulation, CCS) and via carotid artery (peripheral chemoreceptor stimulation, PCS). BP and nerve activity signals were analyzed using a frequency domain approach, based on autoregressive spectral and cross-spectral analysis of heart rate (HR) variability. At baseline, low-frequency (LF, around 0.1 Hz, i.e., MWRO) and high-frequency (HF, synchronous with the respiratory rate) components were present in sympathetic and BP signals, while HR and vagal outflow showed only an HF component. Interestingly, a LF component was observed in vagal outflow during the PCS. These preliminary results support the hypothesis of a “common central oscillatory network” that promotes cardiorespiratory coupling. Supported by PRIN 2007 (NM) and NIH R37 NS019814 Grants.

Topic: Heart Rate Variability and Autonomic Control
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
Thromboelastographic Studies in Cerebral Infarction

Blood coagulability in patients following cerebral infarction was studied utilizing the thromboelastograph (TEG). Cerebral infarction patients from two separate institutions were studied within 24 to 48 hours after onset of stroke. Ninety-four stroke patients from one institution and 109 from another yielded a total stroke population of 203 patients for this study. Fifty-nine age-matched normals were used as a control group. Frequency distribution curves were determined for a TEG ratio of ma/(r + k). The 59 controls exhibited a normal frequency distribution between the values of 1.6 and 4.0. Both groups of stroke patients revealed an increased number of patients with a ratio exceeding 4.0, suggesting a hypercoagulable state exists following cerebral infarction in approximately 29% to 38% of the patients studied.

Topic: Blood properties and coagulation
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Evolution of Undergraduate Research as a Critical Component in the Education of Chemists

An emerging, and still developing, theme has been inclusion of a research experience as a central component of an undergraduate chemistry curriculum. Over a half century ago undergraduate research by a faculty mentor and undergraduate students could be found on islands of exceptional activity that were primarily located in private liberal arts colleges. In the decades that followed, undergraduate research evolved beyond the small college environment to include some, or all, of the following: Addition of a "capstone" undergraduate research experience as a requirement for graduation; Revision of "cookbook" laboratory experiments into "research focused" experiments and inclusion of a semester-long research project within traditional laboratories; Early incorporation of research in the four-year curriculum and expansion to multi-year experiences; Overhaul of the curricular structure so that students progressively encounter more research-intensive courses culminating in a significant research experience that requires the production of a research thesis. These four are not an exhaustive list, but chemistry faculty have been leaders in these, and other revisions that are now impacting many disciplines on college campuses. This chapter will detail the evolution of undergraduate research as a critical component in the education of undergraduate chemistry students and the external and internal forces that have driven this change.

Topic: Career Development and Diversity
Subfield: Safety Research
Field: Social Sciences
Domain: Social Sciences
Fragment(s) of the Past: Archives, Conflicts, and Civic Rights in Algiers, 1830–1870

The first thirty years of the French conquest of Algeria witnessed the large-scale destruction of Algiers’s cultural heritage. Researching the processes by which this came about leads us to consider the conditions of production of two sources that refer to the period before the conquest: Les édifices religieux de l’ancien Alger ( The Religious Edifices of Old Algiers ), by Albert Devoulx, and the “Ottoman collection” of archives initially established by the same figure. This dual archaeology, based on the reconstitution of Devoulx’s activities during his lifetime, reveals a virulent struggle over civic rights and particularly over the appropriation of endowments established by the city’s religious institutions. The sources considered here were part and parcel of this struggle. By paying attention to the claims they set out and the interactions between them, it becomes possible to retrace the disappearance of the mosques of Algiers and to appreciate the true nature of these sources.

Topic: Historical Studies and Socio-cultural Analysis
Subfield: History and Philosophy of Science
Field: Arts and Humanities
Domain: Social Sciences
Articulation without acoustics: A case study of Oneida utterance-final forms

Whether the targets of speech production are primarily articulatory or acoustic has been controversial [Guenther et al., J. Acoust. Soc. Am. 105(5), 2854–2865 (1999)]. While it has been observed that tongue movements occur even in contexts where they may be acoustically obscured [Browman and Goldstein, LabPhonI: 341–376 (1990); Tiede et al., J. Acoust. Soc. Am. 110(5), 2, 2657 (2001)], the question of whether natural languages can systematically encode articulations in the absence of acoustic consequences has remained open. A study was conducted to investigate a purported phonological process in the endangered Oneida (Iroquois) language whereby utterance-final forms exhibit fixed sequences having this property. Ultrasound, video, and acoustic data were collected from two native speakers of Oneida in a field setting. Preliminary results indicate that speakers’ tongue positions are significantly different during different utterance-final vowel articulations despite these vowels being completely inaudible. Results confirm claims that the Oneida phenomenon is in fact a case of articulation without acoustics, and indicate that it is indeed possible for articulations to be retained even in the systematic absence of auditory goals. [Work supported by NSERC.]

Topic: Phonetics and Phonology Research
Subfield: Experimental and Cognitive Psychology
Field: Psychology
Domain: Social Sciences
SU‐FF‐I‐52: Comparison of CR QC Phantoms: The Kodak TQT Program Versus a General Purpose Phantom Program

Purpose: Recently, the American Association of Physicists in Medicine (AAPM) issued two Task Group reports (AAPM Reports 74 and 93) covering acceptance testing and QA for CR systems. An important component of CR QA programs is routine testing of system performance by the technologist. Testing should be simple to perform, be easy to evaluate, and probe most facets of system operation. To this end a quality control phantom for routine testing is recommended. CR QA phantoms can be vendor‐specific, or general purpose for cross‐platform use. We compare our clinical experience with both types of phantom and discuss their relative merits. Method and Materials: The optional Kodak Total Quality Tool (TQT), and associated analysis software, is designed for acceptance testing and routine QA of the Kodak DirectView CR system. Our institution has used the TQT for more than two years. The Fluke EZ CR/DR “DIN” test tool (DTT) is a general purpose phantom incorporating a standard test pattern. The DTT, with an in‐house analysis package, has been used with our Fuji CR systems for over four years. Results: Both phantoms measure parameters recommended by the AAPM reports. A detailed comparison of measurement capabilities including spatial resolution and linearity, exposure linearity and calibration, low contrast resolution, uniformity, and noise and artifact evaluation is presented. The documentation and integrated analysis features of the Kodak QA program led to easy implementation and management. The DTT analysis used standard imaging tools and subjective measures. While the DTT is useful for cross‐platform comparisons, the TQT appears to be more sensitive in detecting potential equipment problems. Conclusion: Advantages of the TQT program include: tests specific to the reading mechanism, an integrated user interface, and acceptance and understanding by service personnel. The non‐proprietary DTT is useful for comparing different systems using a set of standardized measures.

Topic: Radiation Dose and Imaging
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
ER+ metastatic breast cancer: past, present, and a prescription for an apoptosis-targeted future.

The importance and role of the estrogen receptor (ER) pathway have been well-recognized in both breast cancer development and progression. The treatment of choice in women with estrogen receptor-positive metastatic breast cancer (ER+ mBC) is classically divided into a variety of endocrine therapies, with three of the most common being: selective estrogen receptor modulators (SERM), aromatase inhibitors (AI), and selective estrogen receptor degraders (SERD). However, resistance develops in 30-50% of patients treated with these endocrine therapies due to a sophisticated and at times redundant interference at the molecular level between the ER, growth factors, and downstream cell-signaling pathways. Tumor response is heightened with adjunctive therapy that includes an mTORC1 inhibitor (everolimus), CDK4/6 inhibitors (palbociclib/ribociclib/abemaciclib), and an α isoform-specific PI3K inhibitor (alpelisib). Each of these inhibitors elicits potent anti-proliferative benefits; however, they fail to induce tumor cell death. Consequently, disease progression almost invariably occurs. Evasion of apoptosis is a hallmark of cancer. The p53 and BCL2 represent two important nodes of the apoptosis signaling pathway. Venetoclax, a potent and selective BCL2 inhibitor, synergizes with hormonal therapy in ER+ breast cancer models and is active in clinical trials. Similarly, an MDM2 inhibitor, AMG-232, which induces p53 is active in early clinical trials of both liquid and advanced solid tumor patients. In our ER+ BC cohort (Avera Cancer Institute, Sioux Falls, SD), we observed more than 70% of wild type TP53 and over 10% amplification of MDM2 and MDM4 as comparable with the TCGA data set. We summarized current treatment options, the molecular mechanisms that predispose to endocrine resistance, and a future pro-apoptotic treatment strategy for ER+ mBC patients. Our review presents critical analyses of the therapeutic options for the clinical management of ER+ Metastatic Breast Cancer in the light of a hypothesis targeting the induction of apoptosis in p53 wild type tumors. We reviewed not only the FDA approved current treatment approaches but also presented a discourse addressing the possibilities for novel combination strategy that can induce tumor cell apoptosis, a critical cellular mechanism delaying/denying tumor progression. Our review is unique as it presents patient data in support of our hypothesis.

Topic: Advanced Breast Cancer Therapies
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Modelling of disease progression and epidemics

This article presents an attempt to connect pathogen's properties that play an essential role on the cellular level with the results of a pathogen's activity observed on the population level. Since a disease develops in an individual, the features of the pathogen and the individual determine a disease course and outcome. Clearly, individual responses to a pathogen strongly affect the spread of a disease in a population. This leads to our approach of basing the construction of our epidemic model on a disease model that describes a disease course in an individual because this model takes into account both the properties of a pathogen and an individual.

Topic: Evolution and Genetic Dynamics
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Effects of Spinal and Peripheral Injection of α1A or α1D Adrenoceptor Antagonists on Bladder Activity in Rat Models with or without Bladder Outlet Obstruction

Up-regulations of the α1ARs in BOO were observed by the greater increases of BC after α1AR antagonist administrations in the BOO group than in the sham group. However, there were no subtype differences of the α1ARs in functional parameters of bladder activity. In addition, α1ARs also act on the lumbosacral cord which implies that the sensitivity of α1ARs is increased in pathologic models such as BOO. Further evaluation including differential expression of α1ARs in BOO models are need.

Topic: Urinary Bladder and Prostate Research
Subfield: Urology
Field: Medicine
Domain: Health Sciences
Evaluation of special education programs offered in inclusive schools in Saudi Arabia from teachers perspectives

The purpose of this study was to evaluate special education programs that are applied in inclusive schools in Saudi Arabia from teachers perspectives. This study also aimed to discover whether statistically significant differences existed in the opinions of teachers based on their position, gender, teaching experience, and educational level. 615 questionnaires consisting of 20 Likert statements were distributed to a random sample of regular and special education teachers working in inclusive settings in Saudi Arabia. Eighty-five percent (n=523) teachers completed and returned usable questionnaires. An analysis of the collected data, using descriptive statistics and analysis of variance, indicated that the teachers' evaluations for special education programs applied in their schools were generally acceptable. The results also indicated significant differences in the teachers' evaluations based on their position and educational levels, with more positive evaluations found among special education teachers with master's degrees. Furthermore, significant differences were not found in the teachers' evaluations based on gender or amount of teaching experience. (Abdulhade Issa Haimour. Evaluation of special education programs offered in inclusive schools in Saudi Arabia from teachers perspectives. Life Sci J 2013;10(4):57-66). (ISSN: 1097-8135). http://www.lifesciencesite.com. 9

Topic: Disability Education and Employment
Subfield: Safety Research
Field: Social Sciences
Domain: Social Sciences
Unresolved grief in the family.

Unresolved grief after a death in the family may have serious consequences not merely for individuals but for entire families, from grandparents to grandchildren. When the grieving process is abnormal or incomplete, the problem may manifest itself in the physician's office. Observation of a family system can reveal the extent of pathology and the nature of the blocks that keep grief alive. Treatment of unresolved grief ranges from a simple statement of the problem to extended therapy. The physician must be aware of this problem in order to manage it; the cases in this article illustrate presentations of unresolved grief in a variety of family members.

Topic: Grief, Bereavement, and Mental Health
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
Learning From the Past? EU Industrial Policy Challenges

ABSTRACT The European Union's current pursuit of strategic autonomy and technological sovereignty through industrial policy initiatives occurs amid intensifying US‐China competition, prompting new policy instruments and rhetoric that many scholars interpret as fundamental transformation in EU economic governance. However, historical analysis reveals striking parallels with the 1970s–1980s, when Europe confronted US technological dominance and Japanese competition. Drawing on historical institutionalist theory, extensive archival research, and seven interviews with key policymakers from the European Commission, this paper demonstrates how four interconnected structural constraints have maintained the EU's decentralized industrial policy governance across both periods. These constraints create what we term the “Competence Paradox”: external competitive pressures simultaneously create functional demands for centralized coordination while activating national sovereignty protection mechanisms that prevent such centralization. This analysis challenges interpretations of strategic autonomy as institutional transformation, revealing instead how external pressures generate innovation through institutional layering rather than governance transformation.

Topic: Regional Development and Policy
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences