jimnoneill/paper-to-field-training huggingface dataset:
Efficient Algorithms for Drawing Large Genealogy Trees

Field: Computer Science (Physical Sciences)

Efficient Algorithms for Drawing Large Genealogy Trees tackles the visualization of extensive family networks marked by multiple roots, undirected cycle, and missing family information. Conventional tree drawings assume a single root, strict acyclicity, and uniform branching—constraints routinely violated in genealogies. This work first adapts and evaluates foundational graph‐drawing techniques— force‐directed layouts and the Sugiyama layered framework—to assess their fit for genealogical data. Two distinct strategies then address scale and clarity: a clustering approach that aggregates closely related individuals into higher‐level units to reduce displayed complexity, and a novel fractal drawing method that represents each person as a rectangle recursively subdividing its area among descendants. In the fractal method, subdivisions alternate between horizontal and vertical at each generation, and a space‐allocation function ensures larger or important subfamilies receive more room. A complete C++ implementation applies these approaches to synthetic benchmarks and a Habsburg dataset of over 30,000 individuals. The combination of domain-aware adaptations, information-reducing clustering, and recursive subdivision results in efficient, visually coherent algorithms for static visualization of large genealogy trees.
What Works in Therapeutic Prisons: Evaluating Psychological Change in Dovegate Therapeutic Community

Field: Social Sciences (Social Sciences)

Uniquely examining the first purpose-built prison community of its kind, HMP Dovegate Therapeutic Community, this book assesses individual prisoners' progress through therapy and provides an evidence base to support investment into prison-based therapeutic communities. Charting the process of change, the authors highlight the key essentials necessary for prisoners to address their motivations and criminal patterns of behaviour, revealing that strong therapeutic alliances and willingness to ask for help as well as offering help to others are critical. The most comprehensive coverage of therapeutic communities to date, this book will be an important resource for students and practitioners working in prisons and with high-risk offenders, providing recommendations for building the best possible environment for prisoners to enhance their self-esteem, improve their behaviour and establish skills to desist.
Studies Toward the Synthesis of Ineleganolide

Field: Chemistry (Physical Sciences)

The dissertation describes efforts to develop a chemical synthesis of the marine natural product ineleganolide. Chapter 1 of the dissertation focuses on the biological origin of ineleganolide and the interrelationship between ineleganolide and other related norcembranoids natural products including those isolated from species of Sinularia soft corals. In addition to the biosynthesis of ineleganolide, our strategy for the chemical synthesis of the natural products is described. Our synthetic strategy is centered around three key transformations; 1) a diastereoselective Mukaiyama-Michael reaction to join together two complex chiral fragments; 2) an epimerization at the &#945;-position of a lactone by an enolization/kinetic protonation sequence; 3) an intramolecular Mukaiyama-aldol-type cyclization, mediated by the thermal fragmentation of a &#946;-alkoxy vinyl triflate to generate a highly electrophilic oxocarbenium ion. Chapter 2 of the dissertation describes the development of efficient diastereoselective syntheses of the two chiral coupling partners for the convergent Mukaiyama-Michael reaction. Chapter 3 of the dissertation discusses the successful coupling of the two fragments to provide an advanced intermediate toward ineleganolide. This intermediate contains all of the carbons in the natural product, and six out of nine of the stereogenic centers with correct configuration. The remainder of this chapter details our unsuccessful efforts to epimerize the C12 stereogenic center of this intermediate by a lactone enolization and kinetic protonation sequence.In Chapter 4 a modified strategy toward ineleganolide is discussed. We will attempt to open the lactone ring to afford conformation flexibility, hopefully allowing he pivotal cyclization in our synthesis with a substrate that contains the incorrect configuration about the C12 stereocenter. Through great efforts we are able to access substrates to evaluate the key cyclization; however, the instability of each of these substrates forced us to consider alternative methods for the cyclization reaction.Chapter 5 details our efforts to induce the key cyclization toward ineleganolide using an oxidative coupling of enolate equivalents. While we were able to selectively functionalize substrates for this reaction, the pivotal step was never successfully achieved. In the final half of Chapter 5 we observed an unexpected Reformatsky cyclization reaction of an advanced intermediate. This reaction yields a product f natural product-like complexity that may be related to the ineleganolide architecture via a pinacol shift.
MUSE: Marginal Unbiased Score Expansion and Application to CMB Lensing

Field: Mathematics (Physical Sciences)

We present the marginal unbiased score expansion (MUSE) method, an algorithm for generic high-dimensional hierarchical Bayesian inference. MUSE performs approximate marginalization over arbitrary non-Gaussian latent parameter spaces, yielding Gaussianized asymptotically unbiased and near-optimal constraints on global parameters of interest. It is computationally much cheaper than exact alternatives like Hamiltonian Monte Carlo (HMC), excelling on funnel problems which challenge HMC, and does not require any problem-specific user supervision like other approximate methods such as Variational Inference or many Simulation-Based Inference methods. MUSE makes possible the first joint Bayesian estimation of the delensed Cosmic Microwave Background (CMB) power spectrum and gravitational lensing potential power spectrum, demonstrated here on a simulated data set as large as the upcoming South Pole Telescope 3G 1500 deg$^2$ survey, corresponding to a latent dimensionality of ${\sim}\,6$ million and of order 100 global bandpower parameters. On a subset of the problem where an exact but more expensive HMC solution is feasible, we verify that MUSE yields nearly optimal results. We also demonstrate that existing spectrum-based forecasting tools which ignore pixel-masking underestimate predicted error bars by only ${\sim}\,10\%$. This method is a promising path forward for fast lensing and delensing analyses which will be necessary for future CMB experiments such as SPT-3G, Simons Observatory, or CMB-S4, and can complement or supersede existing HMC approaches. The success of MUSE on this challenging problem strengthens its case as a generic procedure for a broad class of high-dimensional inference problems.
Correlations among Soil Properties, Growth Characteristics, and Ginsenoside Contents in Wild-Simulated Ginseng with Different Ages

Field: Agricultural and Biological Sciences (Life Sciences)

Wild-simulated ginseng (WSG) is naturally cultivated in forest environment without any artificial facilities or chemicals. Soil property is one of the major factors affecting the growth and active compound synthesis of vegetation. Therefore, growth characteristics and ginsenoside contents of WSG can be affected by soil properties of the cultivation field. Therefore, the aim of this study was to investigate correlations among soil properties, growth characteristics, and ginsenoside contents of WSG with different ages using Spearman’s coefficient analysis method. It was found that most of growth characteristics of WSG except for rhizome length were significantly increased in 7-year-old WSG for both the above-ground part and root part. Soil pH, and exchangeable cations (Ca, Mg) of 13-year-old WSG cultivation site were significantly higher than those of 4-year-old WSG. However, available phosphate of 4-year-old WSG soil was higher than that of 13-year old WSG soil. Contents of ginsenosides of 4-year-old WSG were higher than those of 13-year-old WSG in the above-ground part. Otherwise, in the root part, contents of ginsenosides of 13-year-old WSG were higher than those of 4-year-old WSG. In correlation analysis, growth characteristics of 4-year-old WSG were correlated with more ginsenoside types. Correlations between soil properties and ginsenoside contents in leaves and roots of WSG with the same age also differed. These results suggest that soil properties play essential role in growth and ginsenoside synthesis of WSG. Based on results of this study, growth characteristics, soil properties, and ginsenoside contents of WSG in different WSG cultivation sites need to be further investigated to identify the most suitable cultivation site for WSG.
Transcriptomic Profile of Peripheral Blood Mononuclear Cells in Sirolimus-Sensitive Acquired Pure Red Cell Aplasia Patients

Field: Medicine (Health Sciences)

Objective: Sirolimus is effective for treatment of acquired pure red cell aplasia (aPRCA). Nevertheless, the immunomodulatory effect of sirolimus on peripheral blood mononuclear cells (PBMCs) from aPRCA remains undetermined. This study aims to investigate the immunomodulatory effect of sirolimus using PBMCs transcriptomics of aPRCA patients. Methods: PBMCs were isolated from treatment-naïve (n = 11) or sirolimus-sensitive aPRCA patients ((n = 11) and then underwent RNA-sequencing. Results: A total of 4060 genes, including 1639 upregulated genes and 2421 downregulated genes were significantly dysregulated in sirolimus-sensitive aPRCA patients compared with treatment-naïve patients. The top ten dysregulated genes were SYTL5, VSNL1, LINC00707, BTBD17, LINC01954 AL445437.1, IGKV1-8, AC090826.1, PRAME and LINC00520, respectively. Among the identified biological processes significantly enriched by dysregulated genes, B-cell-mediated immunity and circulating immunoglobulin-mediated humoral immune responses are the top two dysregulated immune responses in aPRCA patients with sirolimus treatment. Additionally, TNF, CD40, HLA-DRB1, SERPING1, SERPING1, C1QA, IGLL5 and IGHV3-11 were the key modulator in B-cell-mediated immune or circulating immunoglobulin-mediated humoral immune responses in sirolimus-sensitive aPRCA patients. Conclusion: We first provided evidence showing the immunomodulatory effect of sirolimus on PBMCs from patients with aPRCA. Sirolimus can modulate the B-cell-mediated immunity and circulating immunoglobulin-mediated humoral immune responses in aPRCA patients.
[The establishment of a three dimensional PCR screening system and quality evaluation of human YAC library].

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

In order to screen out YAC clones in the CEPH YAC library related to a definite gene, DNA fragment or locus, we need to establish a screening system. This paper includes the establishment of this system and the evaluation of its feasibility. According to the experiments, we suggest that it is better to screen the Mega YAC part of the library at first and put five culture plates as a group. Meanwhile, FISH experiments to assess the quality of CEPH YAC library and the first generation physical map of human genome, Were conducted FISH experiments on 26 YAC clones were carried out. There were 13 clones that were chimeric (about 50%), 6 clones that were mapped by mistake (about 23%). So, there were only 9 clones that were mapped correctly and were not chimeric (about 35%).
A Research on Knowledge Sharing among Air Transportation Professionals

Field: Business, Management and Accounting (Social Sciences)

Purpose – Aviation control, navigation, and aircraft control in the air transportation area are very specialized. Each part is in progress for safety, efficiency, automation, and further. On the other hand co-work among each part including knowledge sharing has been inattentive for many reasons. The purpose of this research is to show how practicians and professionals in the air transportation area perceive the issue of knowledge sharing and to recall the necessity of knowledge sharing in the area. And we try to find ways to activate the knowledge sharing in the area. Research design, data, methodology – For the research, we inquired into whether practicians and professionals think knowledge sharing can effect safe aviation positively or not and what steps are necessary to activate knowledge sharing in the area. We adopted survey method using questionnaires for current practicians and interview for specialists. The survey and interview results were analyzed using regression analysis and AHP method. The interview for specialists and analyzing the results using AHP was to investigate what are the precedence factors to activate the knowledge sharing. Results – First, practicians perceive that knowledge sharing will affect aviation safe positively. Second objective knowledges such as, tower air traffic control procedure of aviation control area, flight principle and structure of aircraft control area, instrument landing system of navigation area, for knowledge sharing of each area were identified. Also the precedence factors such as, knowledge absorbability of personal factor, personal expectation of result of expectation factor, leadership of management of Structure factor, method of knowledge spread of application factor for knowledge sharing were found. Conclusions – Knowledge sharing for practicians and professionals in the aviation area is very important especially from the perspective of safety. However, for various many reasons including the environment of each special area that focusing on their own area, knowledge sharing has not been emphasized. We found that practicians in the area feel that knowledge sharing is necessary and helpful. For it, each practician’s active participation is the most important and many ways such as chatting room to share knowledge are to be developed. And the organization culture should be changed to encourage knowledge sharing.
Transgenic mice expressing human apolipoprotein A-I have sera with modest trypanolytic activity in vitro but remain susceptible to infection by Trypanosoma brucei brucei.

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

Although Trypanosoma brucei brucei fatally infects livestock in much of sub-Saharan Africa, humans are innately resistant to infection, apparently because high-density lipoproteins (HDL) in human serum lyse this unicellular protozoan parasite. Recently, we demonstrated that purified human apolipoprotein (apo) A-I, the major protein (M(r) 28,016) constituent of HDL, had full trypanolytic activity in vitro whereas the apoA-I of cattle and sheep was non-lytic. In the present study, we have sought to confirm the trypanocidal capability of human apoA-I by studying four lines of transgenic mice expressing (supra)physiological serum levels of this polypeptide. Although trypanolysis in vitro by sera from transgenic mice (15.1 +/- 1.3% [mean +/- SEM], n = 30) was considerably less than by human sera (typically 60-80%), it was nevertheless significantly greater than by control sera (8.5 +/- 1.1%, n = 10; P < 0.001) and correlated with the concentration of human apoA-I (r = 0.56, P < 0.001). When trypanosomes were incubated at 37 degrees C with human serum or with human apoA-I for 30 min (i.e., within the pre-lytic period) they lost their ability to subsequently infect mice; trypanosomes incubated with transgenic mice serum remained infective. Furthermore, transgenic mice were fully susceptible to infection when inoculated with 10(3) trypanosomes; both the initial detection of trypanosomes in the blood (3-4 days) and the time to death (5-6 days) were no longer than control mice. This apparent paradox between the action of human apoA-I in human serum and in mouse serum was investigated further.(ABSTRACT TRUNCATED AT 250 WORDS)
Abdominal Wall Recurrence Following Curative Resection of Colorectal Cancer

Field: Medicine (Health Sciences)

腹腔鏡下大腸癌切除後のport site recurrenceが注目されているが, その比較対照となる, 従来の開腹手術後の腹壁再発について検討した報告はきわめて少ない。今回, 当科における大腸癌開腹手術後の腹壁再発についてretrospectiveに検討した。1986年から1999年の間に当科で開腹下に根治度AあるいはBの切除を受け, 2年間以上経過観察し得た大腸腺癌577例のうち, 腹壁再発が確認されたのは3例 (0.52%) であった。これらの病期はDukes' C2例, Dukes' D1例で, 組織学的壁深達度はss (ただしp2) se, si各1例であり, いずれも手術時に遊離癌細胞が腹腔内に存在した可能性が示唆された。腹壁再発を疑うまでの期間は平均16カ月 (14カ月, 6カ月, 29カ月) で, いずれも再発巣の切除が行われたが, その後5～50カ月後に全例腫瘍死した。一方, 深達度mpまでの127例あるいはstage II以下の323例には1例の腹壁再発も認めなかった。
PIGMENTnet: Chlorophyll-b Prediction of Lactuca Sativa Leaf Under Hybrid Genetic Algorithm and Recurrent Neural Network

Field: Computer Science (Physical Sciences)

Chlorophyll content is an imperative indicator of lettuce (Lactuca Sativa) health status. Through computational intelligence, this paper bestowed a noninvasive, accurate, cost-effective ensemble of machine learning algorithms for chlorophyll-b concentration prediction. A total of 107 images of loose-leaf lettuce var. Altima from an aquaponic farm situated in Rizal province in the Philippines was utilized. By employing CIELab color space, the leaf canopies were segmented and extracted with 18-feature predictors. The regression tree ranked and selected 10 selected significant leaf features (spectral: R, G, S, a*, b*, Cr; morphological: canopy area; textural: contrast, correlation, and homogeneity). A fitness function that optimized the recurrent neural network architecture was constructed using GPTIPSv2 which is a symbolic multigene regression (SMGR) tool. This convergence function was the main element in developing a genetic algorithm (GA)-optimized recurrent neural network model considered as the PIGMENTnet. It provides the optimal quantity of neurons in each of the three hidden layers in neural network architecture. A 75-100-10 conglomeration of neurons in each layer was recommended. The RMSE (0.1486), R2 (0.9998), and MAE (0.0751) results of PIGMENTnet surpassed the unoptimized RNN. Based on these findings, it implies that the developed PIGMENTnet is an effective Chl-b concentration predictor as it provided highly accurate and sensitive results than the sole RNN model.
Informing music teaching and learning using movement analysis technology

Field: Health Professions (Health Sciences)

This study explores the utility of movement analysis technology as a means of contributing to a performance pedagogy informed in part by science. Two research questions were investigated: Can biomechanical skills needed for performance on the violin be accurately and objectively characterized and generalized? Can these data be used to inform performance pedagogy to maximize efficiencies and minimize injury? Movement analysis technology was used to study biomechanical phenomena associated with legato bowing on the violin. Results identified and described generalizable characteristics or markers among expert violinists, interactions between right shoulder and elbow, and three discrete tempo-dependent phases of motor control. Such markers may provide new ways of accurately identifying, assessing, and communicating when teaching. Results hold implications for factors related to overuse injuries and underscore the need for more systematic collaborative inquiry into performance pedagogy.
Policy Action for Climate Change Adaptation. Project synthesis report, 2014-2020

Field: Environmental Science (Physical Sciences)

Climate change is increasingly threatening the livelihoods of millions of smallholder farmers in Sub-Saharan Africa. Increased climate variability, including changes in mean temperatures, variation in the onset of rains, and increases in extreme weather events, are directly affecting the growing seasons of commercial and subsistence crops, significantly disturbing socio-economic activities in the agricultural sector and leaving many smallholder farmers in a situation of food insecurity and malnutrition. Within this context, it has become increasingly crucial that governments and relevant stakeholders in the region develop policy strategies that help adapt to changes in climate and help build more resilient food systems. To support these policy processes, the CGIAR Program of Climate Change, Agriculture, and Food Security (CCAFS) started in 2014 the seven-year initiative “Policy Action for Climate Change Adaptation (PACCA)”. PACCA consisted of a first phase (2014-2017), which operated under the project entitled “Influencing and linking national and local level policies and institutions to adopt climate-resilient food systems” in Uganda and Tanzania, and a second phase (2018-2020), which operated under the project entitled “Stimulating adoption of nutrition sensitive climate smart agriculture by aligning national level agenda with implementation” in Uganda and Ethiopia. This report summarizes the main findings that emerged from Phase 1 and 2 of PACCA, presents the lessons learnt and achievements for climate change policy action work and reflects on both projects impact pathways, providing some recommendations for future policy initiatives in the region.
Peripartum opioid exposure impaired maternal behavior, increased inflammatory gene expression, and reduced perineuronal nets in the maternal brain network

Field: Neuroscience (Life Sciences)

7% of pregnant people use opioids. Peripartum opioid use can cause preterm labor, preeclampsia, or pregnancy loss, and opioid withdrawal syndrome in infants. Opioid users are recommended to use medications for opioid use disorder (MOUD), commonly buprenorphine, rather than abstaining, to avoid withdrawal and relapse. Little research has explored the impact opioids and MOUD have on the highly-plastic maternal brain. Opioids have well-established effects on immune signaling in the brain, and we have established that neuroimmune alterations contribute to maternal behavior. Opioids may thus influence the maternal brain by shifting neuroimmune function. We used a rodent model to test how chronic peripartum opioid or MOUD impacted maternal behavior and neuroinflammatory markers. We also examined perineuronal nets (PNNs), extracellular matrix proteins that regulate neuroplasticity. PNNs fluctuate in the maternal brain, and their expression is known to be impacted by opioid exposure and immune activity. PNN fluctuation can be regulated by the action of matrix metalloproteinases (MMPs), which are proteases that can break down ECM components. Female rats were treated with vehicle (VEH), buprenorphine (BUP; 0.3mg/kg/day), or oxycodone (OXY; 10mg/kg/day) prior to pregnancy, throughout pregnancy, and in the postpartum period. We found that opioid mothers displayed deficits in maternal behavior in a pup retrieval task. PNNs were labeled via immunofluorescence across maternal brain regions including: prelimbic prefrontal cortex (plPFC), infralimbic prefrontal cortex (ilPFC), orbitofrontal cortex (OFC), motor cortex (mCTX), dorsal hippocampus (dHPC), amygdala (AMY), and periaqueductal gray (PAG). PNNs decreased in plPFC, ilPFC, OFC, CA2 subregion of dHPC, and PAG in opioid-treated mothers compared to VEH, but no differences were observed in AMY, mCTX, or CA3 and DG subregions of dHPC. Immunerelated transcripts that modulate PNNs, including IL33, MMP2, MMP9, TIMP1, and TLR2, were analyzed via qPCR. In the PFC, MMP2 increased in BUP mothers compared to VEH. In the PAG, TLR2 decreased in BUP mothers compared to VEH. No changes were detected in the AMY. These novel peripartum opioid-induced changes PNN expression and immune signaling in the PFC and PAG could contribute to changes in neural plasticity and behavioral deficits associated with peripartum opioid use, which we will examine in future work.