jimnoneill/paper-to-field-training huggingface dataset:
Integrative Spatial and Transcriptomic Profiling of Tumor Immune Interactions in Lung Cancer

Immune checkpoint inhibitors (ICIs) have reshaped the treatment of non-small cell lung cancer (NSCLC) by harnessing the immune system’s ability to recognize and eliminate tumor cells. While these therapies have led to durable responses in some patients, many fail to benefit, and current biomarkers offer limited prognostic and predictive value. This dissertation leverages advancements in spatial imaging, transcriptomic profiling, and data science to characterize the NSCLC tumor microenvironment and identify spatial and molecular features associated with immune engagement and overall survival. In the first part of this work, I develop and apply a computational pipeline for single-cell analysis of multiplexed immunofluorescence images. This platform enables the quantification of cellular phenotypes, spatial neighborhoods, and tissue architecture, providing a flexible framework for spatial systems immunology. The second part of the dissertation focuses on tumor-intrinsic expression of major histocompatibility complex class II (MHC II) molecules, a pathway with known roles in antigen presentation and immune activation but limited characterization in lung cancer. I integrate multiplexed imaging, spatial transcriptomics, bulk RNA sequencing, and single-cell RNA sequencing to characterize the heterogeneity of MHC II expression in lung adenocarcinoma and assess its relationship with immune microenvironment features, tumor cell states, and patient survival. Together, this body of work advances both computational tools and biological insight into NSCLC immunobiology. It highlights the prognostic relevance of spatially resolved, cell-intrinsic features and offers a framework for future studies aimed at improving patient stratification and informing biomarker development.

Topic: Single-cell and spatial transcriptomics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Competing Social Constructions of Women Workers In Lochner-Era Judicial Decision-Making

Ronald Kahn has argued that the social construction process, which embeds social realities outside the court in legal doctrine, can lead to more rights-protective constitutional interpretations, even during conservative eras. However, especially when particular groups are the subject of multiple or competing social constructions, the social construction process may not always lead to rights-expansive outcomes for disadvantaged groups. From the late 1800s through 1937, state and federal courts struggled to fit women workers into changing legal conceptions of the “right to contract.” Across numerous cases, courts vacillated between two competing social constructions of women workers: women as vulnerable victims in need of special state protections, and women as independent economic actors who were qualified to make their own workplace decisions. Ultimately, social constructions that provided important workplace protections for women workers before 1937 became embedded in legal doctrine in ways that limited their economic and civil equality for decades afterward.

Topic: International Labor and Employment Law
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
Selective dimerization of α-methylstyrene by tunable bis(catecholato)germane Lewis acid catalysts

Donor-ligated bis(catecholato)germanes are highly Lewis acidic and selectively catalyse the dimerization of α-methylstyrene depending on the donor/additive present.

Topic: Organoboron and organosilicon chemistry
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Robust pole placement direct adaptive control

A pole-placement direct adaptive control for not necessarily minimum-phase plants is presented, which is robust with respect to unmodeled dynamics and bounded disturbances. The robustness is achieved by using both a normalized least-squares algorithm with dead zone and appropriate nonlinear feedback. The resulting closed-loop system is shown to be globally stable subject to standard assumptions. >

Topic: Control Systems and Identification
Subfield: Control and Systems Engineering
Field: Engineering
Domain: Physical Sciences
“The Cat’s Paw of Dictatorship”: Police Intelligence and Self-Rule in the Gold Coast, 1948–1952

In 1948, British authorities in the Gold Coast implemented a series of security reforms aimed at resisting future disruptions resulting from growing discontent with colonial rule. These reforms included the formation of a police intelligence organization, developed in collaboration with the British Security Service. This expansion of the colonial state into intelligence work preceded its first steps toward self-rule, inadvertently making this intelligence program an unintended participant in the process of decolonization. This article examines the foundations of that intelligence network and how it resisted the political exigencies required by the Gold Coast’s entry into diarchy. It explains how British officials arrived at the conclusion that a West African colony required a modern, intelligence-gathering apparatus under the oversight of the British Security Service and how that security system was used to challenge the realization of an independent Ghanaian state under the leadership of Kwame Nkrumah.

Topic: African history and culture studies
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences
From sugars to FDCA: a techno-economic assessment using a design concept based on solvent selection and carbon dioxide emissions

Process simulations allow the evaluation of the emissions and selling price for the production of the key monomer FDCA based on different feedstocks and solvent systems, alongside considerations of safety and current process development.

Topic: Catalysis for Biomass Conversion
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
P‐138: Driving Waveforms for Reducing Address Discharge Time Lag in an AC PDP with Auxiliary Electrodes

Abstract The address discharge time lag in an AC PDP with auxiliary electrodes was improved by applying auxiliary pulses and a stepped scan pulse during the address period. Interaction between the auxiliary pulse and the stepped scan pulse generated priming particles during the address period, influencing the address discharge positively. As a result, the minimum address voltage was reduced, and was lower than that of conventional driving waveforms. Furthermore, when the proposed waveforms were applied, the address discharge time lag was improved by 32% compared to that of the conventional driving waveforms with the same address voltage.

Topic: Thin-Film Transistor Technologies
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Developing teacher curriculum design expertise: using the CDC Model in the music classroom

Abstract The purpose of this paper is to discuss the impact of the Curriculum Design Coherence Model (CDC Model – Rata, 2019) on the design practice of two music teachers in a middle school music class in New Zealand. The CDC Model proposes that deep learning first requires deep design coherence. This coherence is generated by three interrelated design dimensions: (i) the ‘surfacing’ of epistemic structure, (ii) the use of subject concepts and (iii) the interrelationship between ‘knowledge-that’ (knowledge of something) and ‘know-how-to’ (knowing how to do something with that knowledge of something). We discuss how the model has been put to use in the design of a song writing unit of work for students aged 10–12 years in a general music class and note the impact of the model on the developing design expertise of the two music teachers involved in a wider research project.

Topic: Educational Theory and Curriculum Studies
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
EFFECTIVENESS OF BIOREEF_BLOCK TECHNOLOGY ON REEF FISH DIVERSITY IN MARINE WATERS OF SUNGAI CUKA VILLAGE AT KINTAP DISTRICT, TANAH LAUT REGENCY OF SOUTH KALIMANTAN, INDONESIA

Bioreef_Block is a modified blend of Bioreeftek with concrete blocks. Bioreef_Block is a medium that uses green technology that utilizes natural materials (coconut shells) which aims as a medium for the attachment of coral planula larvae, with a concrete block foundation in the form of a hollow cube frame with the aim of providing a fish house. This study aims to determine the effectiveness of Bioreef_Block technology on the diversity of reef fish in the sea waters of Sungai Cuka Village, Kintap District, Tanah Laut Regency, South Kalimantan, Indonesia. From the physical and chemical parameters of the water, only the salinity is below the quality standard, this is presumably due to high rainfall. From this study it can be concluded that in general the number of families recorded is 13 families with 18 species of fish found in the vicinity of Bioreef_Block. The composition of the target fish group was 10 families while the major and indicator fish were 2 families, there was an increase in fish abundance at each data collection, the value of the diversity index (H') was small with very strong environmental pressure, but in each observation there was an increase in diversity. The uniformity index (E) before the presence of Bioreef_Block was small with a depressed community, but after the presence of Bioreef_Block in the first month there was a moderate increase in uniformity, with unstable communities, and in the following month observations there was high uniformity with stable communities. Meanwhile, for the dominance index (C) of reef fish, there are no criteria for dominant fish.

Topic: Marine and Coastal Ecosystems
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Book Review: Zionism’s Maritime Revolution: The Yishuv’s Hold on the Land of Israel’s Sea and Shores, 1917–1948

Matthew Hughes, Book Review: Zionism’s Maritime Revolution: The Yishuv’s Hold on the Land of Israel’s Sea and Shores, 1917–1948, International Journal of Maritime History, pp. 502-504. Copyright © 2021 The Author. DOI: https://doi.org/10.1177/0843871420920957b.

Topic: Jewish and Middle Eastern Studies
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Lo(u)st in Therapy: Development and Psychometric Evaluation of the Therapists’ Attitude toward Sexual and Erotic Feelings Scale (TASEF)

This study aimed to develop the Therapists' Attitude toward Sexual and Erotic Feelings (TASEF) scale for assessing therapists' attitudes and responses toward sexual and erotic feelings in therapy. A total of 507 therapists participated in two separate studies. Study 1 focused on finalizing the format of the TASEF and evaluating its construct validity. Through Exploratory Graph Analysis, four factors were identified within the TASEF questionnaire: Gratification, which captures the positive affect experienced by therapists in response to a patient's sexual attraction toward them; Fear, which represents therapists' apprehension or discomfort when encountering sexual feelings from the patient; Threat, which reflects the perception of risk or danger that erotic transference poses to the patient, therapist, and the therapeutic process; and Aversion, which encompasses the therapist's discomfort or aversion toward the patient's sexual feelings. Study 2 aimed to confirm the structure of the TASEF questionnaire and assess its overall validity. The results showed that the TASEF demonstrated adequate overall validity, with higher convergence validity observed for the Fear, Aversion, and Threat clusters compared to the Gratification cluster. The TASEF enables therapists to understand and manage their emotional reactions to sexual feelings in therapy, maintaining standards of care.

Topic: Attachment and Relationship Dynamics
Subfield: Social Psychology
Field: Psychology
Domain: Social Sciences
Modeling of Mass Transfer During Hot-Smoking of Fish Fillets

This work aims at evaluating the mass reduction of traditionally hot-smoked catfish (Arius heudelotii) during hot-air drying unit operation. Drying kinetics of fish fillets are proposed from experimental investigations, taking into account the relative contributions of water evaporation and water and fat drips. The influence of the air temperature (50 to 80_C), air velocity (1 to 3 m/s) and relative humidity (15 to 40%) on drying rate functions is analyzed from a Doehlert experimental design. Based on the identification of characteristic drying rate curves, a drying model is defined and proves to be quite accurate regarding the prediction of evaporation rate during the falling rate period.

Topic: Food Drying and Modeling
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Reversible alkaline inactivation of lignin peroxidase involves the release of both the distal and proximal site calcium ions and bishistidine co-ordination of the haem

Phanerochaete chrysosporium lignin peroxidase isoenzyme H2 (LiP H2) exhibits a transition to a stable, inactive form at pH 9.0 with concomitant spectroscopic changes. The Söret peak intensity decreases some 55% with a red shift from 408 to 412 nm; the bands at 502 nm and 638 nm disappear and the peak at 536 nm increases. The EPR spectrum changes from a signal typical of high spin ferric haem to an exclusively low spin spectrum with g = 2.92, 2.27, 1.50. These data indicate that the active pentaco-ordinated haem is converted into a hexaco-ordinated species at alkaline pH. Room temperature near-IR MCD data coupled with the EPR spectrum allow us to assign the haem co-ordination of alkali-inactivated enzyme as bishistidine. Re-acidification of the alkali-inactivated enzyme to pH 6 induces further spectroscopic changes and generates an irreversibly inactivated species. By contrast, a pH shift from 9.0 to 6.0 with simultaneous addition of 50 mM CaCl2 results in the recovery of the initial activity together with the spectroscopic characteristics of the native ferric enzyme. Incubating with 50 mM CaCl2 at a pH between 6.0 and 9.0 can also re-activate the enzyme. Divalent metals other than Ca2+ do not result in restoration of activity. Experiments with 45Ca indicate that two tightly bound calcium ions per enzyme monomer are lost during inactivation and reincorporated during subsequent re-activation, consistent with the presence of two structural Ca2+ ions in LiP H2. It is concluded that both the structural Ca2+ ions play key roles in the reversible alkaline inactivation of LiP H2.

Topic: Enzyme-mediated dye degradation
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Managing thrombophilia during pregnancy

Thrombophilia is an inherited or acquired predisposition detected by a set of laboratory tests, which increases the risk for venous thromboembolism or pregnancy complications, as will be discussed. Thrombophilia, as with all other risk factors, should be looked for and modulated according to clinical presentation and risk stratification. Many articles have been written on thrombophilia and pregnancy, but this comprehensive article will focus on the issue from a unique perspective of each thrombophilia separately. This article will elaborate on the main types of thrombophilia and will suggest tools to the treating physician for dealing with thrombophilia during pregnancy. This article is the result of a search of the English literature on PubMed using thrombophilia, pregnancy, complications and thrombosis as keywords.

Topic: Blood Coagulation and Thrombosis Mechanisms
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Studies on Effect of Seed Biopriming with MPKV Bacterial Consortium on Growth and Yield of Black Gram

The present investigation was conducted with the objective to study the inoculation effect of seed biopriming with MPKV bacterial consortium on growth and yield of black gram by using the MPKV bacterial consortium during kharif 2022 at the College of Agriculture, Pune. The results of the present investigation revealed that among the different biopriming treatments, seed biopriming with MPKV bacterial consortium + 75% RDF was found to be the most effective as it recorded significantly the highest germination (94.15%), plant height (44.54 cm and 61.45 cm) at floweing and harvest, root length (13.39 cm and 18.97 cm) at floweing and harvest, number of nodules (32.67 plant-1) at flowering, seed yield (9.97 q ha-1) at harvest.

Topic: Plant Disease Management Techniques
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Obesity and menopausal status as determinants of procarcinogenic breast inflammation.

512 Background: Chronic inflammation predisposes to several malignancies. We previously demonstrated an obesity → inflammation → aromatase axis in breast tissue. As obesity is a risk factor for postmenopausal (PoM) but not premenopausal (PreM) breast cancer (BC), we examined whether menopause and body mass index (BMI) independently impact breast white adipose tissue (WAT) inflammation. Methods: WAT was prospectively collected from patients (pts) from 04/10 – 08/13. WAT inflammation, detected by CD68 immunohistochemistry, was defined by the presence of dead/dying adipocytes surrounded by an envelope of macrophages known as crown-like structures of the breast (CLS-B). WAT area was measured with NIH Image J. Adipocyte diameter was measured with Canvas 11 Software. Endpoints: 1) CLS-B (+/-) and 2) CLS-B/cm2. Clinicopathologic associations with CLS-B were analyzed by logistic regression and Fisher’s exact test. Results: WAT (237 mastectomies, 13 abdominal reconstructions) was obtained from 238 women; median age 48 (range 22 – 90). CLS-B occurrence and number of CLS-B/cm2 were greater in overweight/obese (BMI ≥25) and PoM pts compared to lean (BMI <25) and PreM pts (Table). In multivariable analyses, BMI and PoM state were independently associated with CLS-B presence (P<.01 and P=.04) and greater CLS-B/cm2(P<.01 and P=.01). PoM pts had larger mean adipocyte diameter (105.2 +/- 14.0 μ) than PreM pts (95.7 +/- 15.6 μ; P<.01). In pts with bilateral breast WAT and abdominal WAT, concordant CLS status (+/-) was found in 49/63 (78%) and 10/13 (77%) pts, respectively. Conclusions: Breast WAT inflammation (both presence and severity), which we have previously linked to increased aromatase activity, is associated with both increased BMI and menopause. These findings can explain the increased risk of estrogen receptor-positive BC with obesity and PoM status and may also provide targets for rational therapies. Feature CLS-B – N, (%) CLS-B + N, (%) P CLS-B/cm2Median, (range) P Lean (N=116) 76 (66%) 40 (34%) .27 (.06 – 4.37) Overweight (N=73) 34 (47%) 39 (53%) .26 (.05 – 51.85) Obese (N=48) 5 (10%) 43 (90%) <.01 .47 (.09 – 2.35) .01 Premenopausal (N=144) 80 (56%) 64 (44%) .26 (.05 – 5.49) Postmenopausal (N=93) 35 (38%) 58 (62%) <.01 .49 (.09 – 51.85) <.01

Topic: Cancer Risks and Factors
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
ANALYSIS OF INDUCED ISOMETRIC FATIGUING CONTRACTIONS IN BICEPS BRACHII MUSCLES USING MYOTONOMETRY AND SURFACE ELECTROMYOGRAPHIC MEASUREMENTS

Viscoelastic properties of skeletal muscle tissue are known to be impacted by fatiguing contractions. In this study, an attempt has been made to utilize myotonometry for analyzing the relationship between muscle viscoelasticity and contractile behaviors in a fatiguing task. For this purpose, thirteen young healthy volunteers are recruited to perform the fatiguing isometric task and the time to task failure (TTF) is recorded. Myotonometric parameters and simultaneous surface electromyographic (sEMG) signals are recorded from the Biceps Brachii muscle of the flexed arm. The correlation between myotonometric parameters and TTF is further analyzed. Cross-validation with sEMG features is also performed. Stiffness of muscle has a positive correlation with TTF in the left hand ([Formula: see text]). Damping property of the nonfatigued muscle is positively associated with the fatigue-induced changes in amplitude features of sEMG signal in the right hand ([Formula: see text]). The normalized rate of change of mean frequency of sEMG signal has a positive correlation with stiffness values in both of the hands ([Formula: see text]). Muscle viscoelasticity is demonstrated to influence the progression of fatigue, although the difference in motor control due to handedness is also found to be an important factor. The results are promising to improve the understanding of the effect of muscle mechanics in fatigue-induced task failure.

Topic: Muscle activation and electromyography studies
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
[Post-operative respiratory function after subcutaneous and epidural morphine analgesia (author's transl)].

In 20 elderly patients who underwent cholecystectomy post-operative analgesia was obtained with morphine given either subcutaneously (n = 10) or epidurally (n = 10). Both groups were comparable as to age and pre-operative respiratory function values. On the first post-operative day, vital capacity, forced expiratory volume in one second and and paO2 were significantly higher in the epidural morphine group (respectively 70 +/- 6 p. cent and 68 +/- 6 p. cent of pre-operative values, and 74 +/- 3 mmHg) (mean +/- s.e.m.) than in the subcutaneous morphine group, where the corresponding figures were 52 +/- 4 p. cent, 48 +/- 5 p. cent and 63 +/- 2 mmHg respectively. PaCO2 was unchanged in both groups. These data indicate that epidural morphine analgesia to some extent reduces the post-operative respiratory dysfunction observed after abdominal surgery.

Topic: Anesthesia and Pain Management
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Genotyping Hepatitis Virus: New Developments and Clinical Impact

The First Miyakawa Memorial Research Foundation (MMRF) Meeting on Viral Hepatitis held in Tokyo in January 2003 focussed on the clinical relevance of HBV genotypes in the manifestation of chronic liver disease as well as the development of new antiviral treatment of chronic hepatitis B. Since the late 1990s, chronic hepatitis B has been treated

Topic: Hepatitis B Virus Studies
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Business Cycle Indication Using Query Logs of Search Engines

Identifying status of business cycles is critical to governments and enterprises when building business strategies. Traditionally, economic variables, such as industrial production, stock price index, manufacturing sales, are selected to compose business cycle indicators, which altogether evaluate business cycle status. In general, the release of economic variables involves long data processes that delay the announcement of business status. The announced business status thus is not timely and could increase the uncertainty of business decision making. In this work, we employ query logs of search engines for business cycle identification. As query logs are readily available through online Web services, they can provide timely and accurate information about business status. We propose a feature selection method to identify query terms appropriate for business cycle identification. Evaluation results show that the identified query terms are effective indicators and the proposed method models business cycles correctly.

Topic: Time Series Analysis and Forecasting
Subfield: Signal Processing
Field: Computer Science
Domain: Physical Sciences