jimnoneill/paper-to-field-training huggingface dataset:
From meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer

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

The human gastrointestinal tract is home for trillions of bacteria that influence homeostasis and health in a complex biological system: the gut microbiome. Accumulating evidence suggests that a state of pathological imbalance in the microbiome (dysbiosis) is present in patients suffering from colorectal cancer (CRC). To date, microbiome studies identified specific bacteria being associated with dysbiosis in CRC. Some of these bacteria (e.g. Fusobacteria) directly or indirectly interact with cancer and immune cells of their host. However, current studies only focused on certain microbes in detail, hence, their role in the etiology of the disease remains elusive. Accordingly, my project investigates the role of CRC-associated bacteria in tumor initiation and progression while addressing the question: which and what kind of microbes interact with, favor, or can cause CRC? In a first step, we identified CRC-associated bacteria, enriched at the tumor site of Luxembourgish CRC patients. By using Fusobacterium nucleatum as our study model, we predicted and optimized bacterial growth (media) in silico by using a genome-scale metabolic reconstruction model for a constraint-based modelling approach. Next, we assessed bacterial growth and metabolism in the optimized growth medium by using flow cytometry and mass spectrometry. Finally, we co-cultured the bacteria together with primary patient-derived cultures in the recently developed, microfluidics-based, human-microbial cross-talk model (HuMiX) [1]. As part of our ongoing validations, we infected patient-derived, healthy and cancerous 3D colonic organoids with our bacterial candidate. This workflow enables us to analyze pro-tumorigenic capacities of CRC-associated bacteria on healthy and cancerous colonocytes. It will serve as a promising tool for future analysis of host-microbial interaction mechanisms of various CRC-associated bacteria on a transcriptomic, proteomic, and metabolomic level. [1] Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K et al. (2016) A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nature communications 7: 11535.
The language of the accounting ledger journal of the church of the holy apostles Peter and Paul in Arad (1728‒1752) - phonological features

Field: Arts and Humanities (Social Sciences)

The paper analyzes certain phonological characteristics of the Accounting Ledger Journal of the Church of the Holy Apostles Peter and Paul, the document that has been kept under this name in the said church in Arad (under the signature INV 794). The document contains two protocols: the first one that was kept from 1728 until 1782 and the second one kept from 1776 until 1790. This paper analyzes the corpus from the first half of the 18th century (more precisely, the time period from 1728 until 1752). Since this is a text that encompasses two periods on the timeline: (1) the period in which Russian-Slavonic substituted Serbian-Slavonic and (2) the period in which Slavonic-Serbian was established and in which it existed - the basic task of this research is the identification of the language in which the Accounting Ledger Journal was written. In the paper, special attention is paid to the relation between vernacular and literary elements in the analyzed document, as well as to the dependence of their use on various contextual parameters. The analysis of the selected phonological characteristics of the Accounting Ledger Journal of the Church of the Holy Apostles Peter and Paul (1728-1752) indicates the chronological matching with the data from previous research of documents with a similar profile on the territory of South Hungary. The fourth and fifth decade is, in fact, the time that saw a more prominent penetration of Russian-Slavonic elements into manuscripts. Their number, however, is not large enough to regard it as a mixed language. The Accounting Ledger Journal as a whole still had a vernacular basis, which confirms the previous assumption concerning the elitization of folk language as the basic model for creating the Slavonic-Serbian language in the manuscripts of the 18th century. The analysis also shows that literary features (Serbian-Slavonic and Russian-Slavonic) were conditioned primarily by the thematic and structural organization of the text, as well as the social stratification of the people mentioned in the aforementioned document.
The Cyclopteris of Laveineopteris (Late Carboniferous pteridosperm). Fancies and facts: methodological and taxonomical implications

Field: Earth and Planetary Sciences (Physical Sciences)

Cyclopterid folioles commonly borne on the fronds of Late Carboniferous neuropterid plants were recently interpreted as entire shade leaves that were, among the taxa exhibiting a neuropteroid pinnate foliage, only present in the medullosalean genus Laveineopteris. Numerous speculations concerning the physiology, growth habit, ecology and the reconstruction of the Laveineopteris plant were derived from this assertion. It is shown in this paper that this assertion is inaccurate. Cyclopterids are not entire leaves. They are heteromorphic folioles confined to the fronds, and mainly located in the proximal parts of them. They are homologous to ultimate pinnae sometines being slightly bipinnatifid at the base. In addition to a photosynthetic role, cyclopterids were also playing a protective role for the circinately coiled pinnate foliage segments during the early differentiation of the fronds. It is also shown that cyclopterids are not restricted to the sole genus Laveineopteris among the neuropterids. The cuticular information on which several recent taxonomic treatments of the neuropterids were based is critically analyzed and found inadequate. The diagnoses of several neuropterid taxa are emended.
The extremal spectral radii of $k$-uniform supertrees

Field: Mathematics (Physical Sciences)

In this paper, we study some extremal problems of three kinds of spectral radii of $k$-uniform hypergraphs (the adjacency spectral radius, the signless Laplacian spectral radius and the incidence $Q$-spectral radius). We call a connected and acyclic $k$-uniform hypergraph a supertree. We introduce the operation of "moving edges" for hypergraphs, together with the two special cases of this operation: the edge-releasing operation and the total grafting operation. By studying the perturbation of these kinds of spectral radii of hypergraphs under these operations, we prove that for all these three kinds of spectral radii, the hyperstar $\mathcal{S}_{n,k}$ attains uniquely the maximum spectral radius among all $k$-uniform supertrees on $n$ vertices. We also determine the unique $k$-uniform supertree on $n$ vertices with the second largest spectral radius (for these three kinds of spectral radii). We also prove that for all these three kinds of spectral radii, the loose path $\mathcal{P}_{n,k}$ attains uniquely the minimum spectral radius among all $k$-th power hypertrees of $n$ vertices. Some bounds on the incidence $Q$-spectral radius are given. The relation between the incidence $Q$-spectral radius and the spectral radius of the matrix product of the incidence matrix and its transpose is discussed.
Human capital externalities and growth

Field: Economics, Econometrics and Finance (Social Sciences)

This paper proposes a methodology to estimate externalities in human capital as a response to the evidence of a worldwide divergent development. We estimate supply and demand for human capital in a five-year panel for 60 countries in the period 1980-2000, and found that there are positive externalities in human capital accumulation close to one, implying increasing returns to scale and increasing marginal returns in human capital which eliminates the channel that enables generating conditional convergence.
Improved Doppler Shift Estimation Algorithm for Down-Link Signals of Space-Based AIS

Field: Computer Science (Physical Sciences)

As an enhanced system for marine monitoring and autonomous navigation, the space-based automatic identification system (AIS) has attracted extensive attention and become a hot topic for research. However, it encounters the problem of Doppler shift stemmed from the relative motion between satellites and ships, which leads to performance degradation. To circumvent this issue, in this correspondence, we propose an improved Doppler shift estimation algorithm for down-link signals of space-based AIS, utilizing the calculation of the autocorrelation and ratio on the Rice factor. Specifically, the addressed method is robust to the non-Gaussian noise. Further, the suggested approach has low complexity compared with the existing algorithm. Finally, numerical simulations, such as the standard deviation of the estimated Doppler shift versus signal-to-noise ratio, Rice factor and non-Gaussian noise, and the complexity comparisons, are carried out to validate the theoretical analysis, and demonstrate the superior performance of the proposed estimation approach.
Gastroenterology in Motion

Field: Medicine (Health Sciences)

Endoscopic submucosal dissection (ESD) has developed into an accepted therapy for early gastroinestinal neoplasia, especially in Asian countries.1– 4 A ajor benefit of ESD is that it allows en bloc resection nd, thus, decreases risk of neoplastic recurrence.5 Western endoscopists have not embraced ESD techniques nearly as readily as their Eastern counterparts. This is likely due to a multitude of factors including low incidence of gastric malignancies, less exposure to ESD training, reimbursement issues, lengthy procedural times, and higher complication rates as compared to endoscopic mucosal resection (EMR).6 Methods that simplify the steps associated with ESD may help to proliferate its use. A new endoscopic gel (Cook Medical Inc, Winston-Salem, NC) was recently developed. This viscous gel was introduced for submucosal injection prior to excision of lesions of the gastrointestinal tract as the lesions are lifted by a visible bleb. Our exploratory laboratory experiments suggested that the gel also has tissue dissecting properties. Here, we present our initial experience with the use of this novel gel for facilitating submucosal dissection during gastric ESD.
Digital Marketing Innovation for MSMEs through ChatGPT Integration and Management Information Systems: A Technological Transformation Approach for Competitive Advantage

Field: Business, Management and Accounting (Social Sciences)

Micro, Small, and Medium Enterprises (MSMEs) play a significant role in Indonesia's economy. However, with technological advancements and changing consumer trends, MSMEs face substantial challenges in maintaining and enhancing their competitiveness. The development of digital technology is an imperative that cannot be ignored if MSMEs are to remain relevant and competitive in the modern era. This research examines how the integration of ChatGPT and Management Information Systems (MIS) can positively impact the digital marketing of MSMEs and how these enterprises can leverage this technology to enhance their competitiveness. This study employs a literature review method with a qualitative approach. Data were obtained from Google Scholar covering the period from 2014 to 2024. The results indicate that digitalization, through the implementation of technologies such as ChatGPT and Management Information Systems, significantly impacts MSMEs by enhancing their competitiveness. Integrating ChatGPT with MIS not only improves operational efficiency but also enriches customer experience through more responsive and personalized services. Case studies from companies like Tokopedia, Zalora, and Kopi Kenangan demonstrate that adopting digital technology can expand market reach, increase sales, and improve stock management. However, challenges such as infrastructure limitations and the need for staff training must be addressed to ensure successful technology adoption. The long-term success of digital technology highlights the importance of sustainable investment and adaptation to evolving market trends.
Do Adoptions of International Financial Reporting Standards Enhance Capital Investment Efficiency?

Field: Economics, Econometrics and Finance (Social Sciences)

We examine whether adoptions of International Financial Reporting Standards (IFRS) enhance capital investment efficiency, a purported benefit. Data for 10,340 adoptions across 26 countries during 2001-08 reveal mandatory but not voluntary IFRS adoptions to be significantly associated with enhanced capital investment efficiency measured by investment-cash flow sensitivity and value-enhancing risk taking. In contrast to prior findings for capital market effects of IFRS adoptions, associations between mandatory IFRS adoptions and capital investment efficiency are stronger in countries with weaker legal protections, more concentrated ownership, and prior reporting standards that differ more from IFRS. Combined, these findings lend support to mandatory but not voluntary IFRS adoptions serving to enhance firm-level capital investment efficiency, particularly in countries with weaker investor protections.
Bases of Decision in Language Training

Field: Psychology (Social Sciences)

When selecting grammatical structures to use as language development goals in training language-disordered children, the language clinician may refer to various theoretical approaches. Six bases of decision for language training, each following from differing theoretical approaches, are discussed and reviewed: (1) the structural complexity basis, (2) the developmental language basis, (3) the perceptual strategy basis, (4) the mean-length-of-utterance basis, (5) the cognitive basis, and (6) the dialectal basis. Of these possible bases of decision, the developmental language basis, the cognitive basis, the perceptual strategy basis, and the dialectal basis appear to suggest the most useful guidelines for sequences in language training. The language clinician may be able to organize his training program more effectively by recognizing the theoretical bases from which his decisions arise.
Integration of enrichment and accumulation process for Polyhydroxybutyrate production by utilizing wastes from sewage works with mixed microbial culture

Field: Environmental Science (Physical Sciences)

Polyhydroxybutyrate (PHB) is a biodegradable polyester produced by microorganisms as an intracellular carbon and energy reserve. Its biodegradability and biocompatibility make it a promising alternative to conventional petroleum-based plastics. However, the commercialization of PHB is hindered by high production costs, particularly those associated with sterilization and the use of pure carbon sources. This thesis aims to address these financial barriers by utilizing mixed microbial cultures (MMC) and waste materials as carbon sources and simplifying the production process by integrating enrichment and accumulation process.
The thesis comprises three papers that collectively evaluate potential methods for improving PHB production process. The focus is on the use of MMC and sewage waste, as well as on the integration of the PHB enrichment and accumulation processes to streamline production.
Paper I explores how activated sludge from wastewater treatment plants can be enriched to accumulate PHB. The study analyses the impact of operational parameters, such as organic loading rate (OLR) and settling time, on PHB accumulation. The results indicate that shorter settling times lead to the disintegration of granular sludge but enhance PHB accumulation, while higher OLR increases both biomass concentration and PHB content. These findings offer operational guidelines for future research.
Paper II introduces a novel approach to integrating PHB enrichment and accumulation through nutrient decoupling. The study uniquely evaluates the impact of different nutrient decoupling strategies on PHB production while maintaining a constant feast to famine ratio (F/F). The results reveal that both ammonium and phosphate decoupling have similar effects on PHB content at the end of the feast phase. However, PHB productivity and yield can be enhanced through specific decoupling strategies. The paper also delves into the relationship between microbial community structure and PHB production.
Paper III extends the research by examining the effects of various settling strategies on sludge settleability while maintaining PHB accumulation. The study investigates changes in extracellular polymers (EPS) and their correlation with settleability and PHB levels. The results show that introducing a settling phase after the feast phase improves sludge settleability and dewaterability without compromising PHB levels. A shift in the microbial community from Nitrincola to Thauera was also observed, correlating with improved settleability.
In summary, this thesis introduces innovative approaches to PHB production by integrating enrichment and accumulation processes. By employing unique nutrient decoupling and settling strategies with a fixed F/F ratio, it addresses existing knowledge gaps. It is hoped that these efforts will significantly contribute to the advancement of PHB production.
[The role of surgery in comprehensive treatment of spinal neoplasms].

Field: Medicine (Health Sciences)

Basing on clinical experience of 212 surgically treated spinal tumours the authors present the principal problems in surgical treatment of neoplasmatic disease of the spine. The essential aim of surgical treatment is the tendency to the radical removal of the tumour and, in the same time, to achieve a good stabilization of the spine. The best method of stabilization of the spine is internal stabilization, transpedicular and interbody. The removed parts of the vertebral column should be replaced with bone grafts. The surgical treatment should be combined with oncological and rehabilitation.
Construction of recombinant adenoviral pShuttle-CMV plasmid containing multiple genes of FMDV

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

Two recombinant adenoviral pShuttle-CMV plasmid containing FMDV type O capsid , 3C protease and 3D polymerase coding regions were constructed by the methods of multi-step cloning and ligating PCR. The recombinant pShuttle-CMV plasmids were confirmed by PCR,digestion of restricted endonuclease and sequencing.These recombinant pShuttle-CMV can be used to create recombinant adenovirus containing FMDV capsid and no-structural protein genes.
Evaluation of Antioxidant Capacity and Safety Profile of Selected Medicinal Plant Extracts.

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

ABSTRACT: Medicinal plants are widely recognised for their medicinal benefits, notably due to their bioactive phytochemicals and antioxidant capacity. The aim of the study is to investigate the phytochemical composition, antioxidant activity and cytotoxic effect of medicinal plants Ferula asafoetida Linn., Hyoscyamus niger Linn, Matricaria chamomilla Linn, Styrax benzoin Dryland., and Sesamum indicum Linn. Hydroalcoholic extracts of the medicinal plants were extracted using Soxhlet apparatus. Phytochemical screening was performed to identify the secondary metabolites. Quantitative analysis of protein, carbohydrates, total phenolic content (TPC) and flavonoids content (TFC). Antioxidant activity was evaluated using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay, 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, the nitric oxide (NO) scavenging assay, Lipid peroxidation assay, ferric reducing antioxidant power assay and DNA damage protection against the oxidative stress induced by hydrogen peroxide. The toxicity evaluation is measured by the HET-CAM (Hen’s Egg Test – Chorioallantoic Membrane) assay. The functional group detection is done by the FTIR (Fourier Transform Infrared) spectroscopy for better exposure to the identification of bioactive compounds. The results show that the phytochemical content of these plant extracts is dose dependent as the concentration of these extracts increases the phytochemical increase and eventually the antioxidant activity also increases. This notable behavior of these extracts aligns with the published data and suggests the efficiency of these plants in terms of therapeutics and health care.
Web-based Soybean Yield Simulation Model to Analyze the Effects of Interacting Yield-Limiting Factors

Field: Agricultural and Biological Sciences (Life Sciences)

WebGro is a web-based soybean decision support system (DSS) built on the CROPGROSoybeanmodel. The purpose of WebGro is to help soybean producers in the Midwestern UnitedStates understand how different stresses interact to limit soybean yield in their fields. Stressesinclude water, soybean cyst nematode, herbicide injury, Rhizoctonia root rot disease and haildamage. The user can set up a field scenario by selecting cultivar, planting date, plant population,soil type and the nearest weather station using a web form. Different stress levels can then beentered and the model can be run interactively by simulating the effects of one or more stresses at atime. The user can evaluate the yield loss relative to running the model with all stresses turned off(yield potential) to determine the effect of different combinations of stresses on yield. WebGro isavailable at http://webgro.ae.iastate.edu.
Aerodynamic Characteristics of Perforated Plates : 1st Report, Resistance Coefficient

Field: Engineering (Physical Sciences)

千鳥形配列に孔をあけた多孔板に一様流を流入させてその抵抗係数を測定し、それが多孔板の開口比と厚比にどのように依存するかを実験的に明らかにした。その結果、抵抗係数は開口比によって大きく変化するばかりでなく、厚比によってもかなり変化し、厚比が1付近を境にその特性が全く異なることを見いだした。そして、流れ学的考察に基づき、抵抗係数を開口比と厚比によって計算できる精度のよい実験式を導いた。
Epidemiological, clinical and genetic aspects of adult onset isolated focal dystonia in Ireland

Field: Medicine (Health Sciences)

Background Adult onset idiopathic isolated focal dystonia presents with a number of phenotypes. Reported prevalence rates vary considerably; well‐characterized cohorts are important to our understanding of this disorder. Aim To perform a nationwide epidemiological study of adult onset idiopathic isolated focal dystonia in the Republic of Ireland. Methods Patients with adult onset idiopathic isolated focal dystonia were recruited from multiple sources. Diagnosis was based on assessment by a neurologist with an expertise in movement disorders. When consent was obtained, a number of clinical features including family history were assessed. Results On the prevalence date there were 592 individuals in Ireland with adult onset idiopathic isolated focal dystonia, a point prevalence of 17.8 per 100 000 (95% confidence interval 16.4−19.2). Phenotype numbers were cervical dystonia 410 (69.2%), blepharospasm 102 (17.2%), focal hand dystonia 39 (6.6%), spasmodic dysphonia 18 (3.0%), musician's dystonia 17 (2.9%) and oromandibular dystonia six (1.0%). Sixty‐two (16.5%) of 375 consenting index cases had a relative with clinically confirmed adult onset idiopathic isolated focal dystonia (18 multiplex and 24 duplex families). Marked variations in the proportions of patients with tremor, segmental spread, sensory tricks, pain and psychiatric symptoms by phenotype were documented. Conclusions The prevalence of adult onset idiopathic isolated focal dystonia in Ireland is higher than that recorded in many similar service‐based epidemiological studies but is still likely to be an underestimate. The low proportion of individuals with blepharospasm may reflect reduced environmental exposure to sunlight in Ireland. This study will serve as a resource for international comparative studies of environmental and genetic factors in the pathogenesis of the disorder.