Miracle-dz/UniFAR-FTUs huggingface dataset:
exKidneyBERT: a language model for kidney transplant pathology reports and the crucial role of extended vocabularies

Background Pathology reports contain key information about the patient’s diagnosis as well as important gross and microscopic findings. These information-rich clinical reports offer an invaluable resource for clinical studies, but data extraction and analysis from such unstructured texts is often manual and tedious. While neural information retrieval systems (typically implemented as deep learning methods for natural language processing) are automatic and flexible, they typically require a large domain-specific text corpus for training, making them infeasible for many medical subdomains. Thus, an automated data extraction method for pathology reports that does not require a large training corpus would be of significant value and utility. Objective To develop a language model-based neural information retrieval system that can be trained on small datasets and validate it by training it on renal transplant-pathology reports to extract relevant information for two predefined questions: (1) “What kind of rejection does the patient show? ”; (2) “What is the grade of interstitial fibrosis and tubular atrophy (IFTA)? ” Methods Kidney BERT was developed by pre-training Clinical BERT on 3.4K renal transplant pathology reports and 1.5M words. Then, exKidneyBERT was developed by extending Clinical BERT’s tokenizer with six technical keywords and repeating the pre-training procedure. This extended the model’s vocabulary. All three models were fine-tuned with information retrieval heads. Results The model with extended vocabulary, exKidneyBERT, outperformed Clinical BERT and Kidney BERT in both questions. For rejection, exKidneyBERT achieved an 83.3% overlap ratio for antibody-mediated rejection (ABMR) and 79.2% for T-cell mediated rejection (TCMR). For IFTA, exKidneyBERT had a 95.8% exact match rate. Conclusion ExKidneyBERT is a high-performing model for extracting information from renal pathology reports. Additional pre-training of BERT language models on specialized small domains does not necessarily improve performance. Extending the BERT tokenizer’s vocabulary library is essential for specialized domains to improve performance, especially when pre-training on small corpora.
Mining Causal Association Rules

Discovering causal relationships is the ultimate goal of many scientific explorations. Causal relationships can be identified with controlled experiments, but such experiments are often very expensive and sometimes impossible to conduct. On the other hand, the collection of observational data has increased dramatically in recent decades. Therefore it is desirable to find causal relationships from the data directly. Significant progress has been made in the field of discovering causal relationships using the Causal Bayesian Network (CBN) theory. The applications of CBNs, however, are greatly limited due to the high computational complexity. In another direction, association rule mining has been shown to be an efficient data mining means for relationship discovery. However, although causal relationships imply associations, the reverse does not always hold. In this paper we study how to use an efficient association mining approach to discover potential causal rules in observational data. We make use of the idea of retrospective cohort studies, a widely used approach in medical and social research, to detect causal association rules. In comparison with the constraint-based methods within the CBN paradigm, the proposed approach is faster and is capable of finding a cause consisting of combined variables.
After the gold rush: toward sustainable scholarship in computing

In just thirty years, we have gone from punched cards to Second Life. But, as the American National Science Foundation (NSF) recently noted, "undergraduate computing education today often looks much as it did several decades ago" (NSF, 2006). Consequently, today's "Nintendo Generation" have voted with their feet. We bore them. The contrast between the changes wrought via computer research over the last 30 years, and the failure of computing education to adapt to those changes, is because computing academics lead a double life. In our research lives we see ourselves as part of a community that reaches beyond our own university. We read literature, we attend conferences, we publish, and the cycle repeats, with community members building upon each other's work. But in our teaching lives we rarely discuss teaching beyond our own university, we are not guided by any teaching literature; instead we simply follow our instincts. Academics in computing, or in any other discipline, can approach their teaching as research into how novices become experts. Several recent multi-institutional research collaborations have studied the development of novice programmers. This paper describes some of the results from those collaborations. The separation of our teaching and research lives diminishes not just our teaching but also our research. The modern practice of stripping away all 'distractions' to maximize research output is like the practice of stripping away rainforest to grow beef -- both practices appear to work, for a little while, but not indefinitely. Twenty-first century academia needs to bring teaching and research together, to form a scholarship of computing that is an integrated, sustainable, ecological whole.
Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69

ABSTRACT The genomes of bacteriophages T4 and RB69 are phylogenetically related but diverge in nucleotide sequence at many loci and are incompatible with each other in vivo. We describe here the biological implications of divergence in a genomic segment that encodes four essential DNA replication proteins: gp45 (sliding clamp), gp44/62 complex (clamp loader), and gp46 (a recombination protein). We have cloned, sequenced, and expressed several overlapping segments of the RB69 gene 46-45.2-(rpbA)-45-44-62cluster and compared its features to those of the homologous gene cluster from T4. The deduced primary structures of all four RB69 replication proteins and gp45.2 from this cluster are very similar (80 to 95% similarity) to those of their respective T4 homologs. In contrast, the rpbA region (which encodes a nonessential protein in T4) is highly diverged (∼49% similarity) between the two phage genomes and does not encode protein in RB69. Expression studies and patterns of high divergence of intercistronic nucleotide sequences of this cluster suggest that T4 and RB69 evolved similar transcriptional and translational control strategies for the cistrons contained therein, but with different specificities. In plasmid-phage complementation assays, we show that posttranslationally, RB69 and T4 homologs of gp45 and the gp44/62 complex can be effectively exchanged between the two phage replicase assemblies; however, we also show results which suggest that mixed clamp loader complexes consisting of T4 gp62 and RB69 gp44 subunits are not active for phage DNA replication. Thus, specificity of the gp44-gp62 interaction in the clamp loader marks a point of departure between the T4 and RB69 replication systems.
Ionic Permeability of the Inhibitory Postsynaptic Membrane of Lobster Muscle Fibers

Reversal potentials (E IPSP) of the inhibitory postsynaptic potential and the membrane resting potentials (EM) of lobster muscle fibers were determined with intracellular recording under a variety of ionic conditions. E IPSP is solely dependent on the electromotive force of anionic batteries; i.e., on the electrochemical gradient for a "mobile" fraction of intracellular Cl (Cli) which is considerably smaller than the total intracellular Cl. The active inhibitory membrane is more permeable to certain "foreign" anions in the order NO3 > SCN > Br > Cl. The membrane is impermeable to BrOs, isethionate, and methylsulfate, but is slightly permeable to acetate and propionate. The level of Cli appears to be determined in part by some active (pump? ) process and most of the anions studied appear to interfere with the steady-state level of Cli.
Depression Screening in the Pregnant Soldier Wellness Program

Objectives: The purpose of this study was to determine the prevalence of depression among active-duty low-risk pregnant women using the Edinburgh Postnatal Depression Scale. Rates for depression have been reported to be as high as 13% during pregnancy and 12 to 22% postpartum, with postpartum suicidal ideation at nearly 7%. Methods: From April 2002 through March 2003, 82 women receiving prenatal care at Madigan Army Medical Center completed screening questionnaires during pregnancy and/or postpartum visits. Results: A total of 97 questionnaires were administered (71 antepartum and 26 postpartum). During pregnancy, 24% of individuals screened scored positive. During the postpartum, 19% scored positive. A total of 15 women were screened twice during the study period. One woman was screened twice during pregnancy and the remaining 14 were screened once antepartum and once postpartum. Suicidal ideation was present in 11% of those screened during pregnancy and in 15% postpartum. Conclusions: Active-duty women appear to have a higher rate of depression and suicidal ideation compared with rates in nonmilitary populations; perhaps such screening should become a standard practice.
A Theory of Freedom: From the Psychology to the Politics of Agency

Introduction . 1. Conceptualizing Freedom. 2. Freedom as Rational Control. 3. Freedom as Volitional Control. 4. Freedom as Discursive Control. 5. Freedom and Collectivization. 6. Freedom and Politicization. 7. Freedom and Democratization. 8. Conclusion. References
Questioning the New Public Management

Contents: Introduction: questioning the new public management, Mike Dent, John Chandler and Jim Barry. Context and Theory of the New Public Management: New public management and the professions in the UK: reconfiguring control? , Mike Dent and Jim Barry. Variations Between Sectors: Does 'Best Value' represent best value? local government middle management perspectives, Linda Keen What do we want from social care managers? aspirations and realities, Jeanette Henderson and Janet Seden Have you seen my assessment schedule? Proceduralization, constraint and control in social work with children and families, Paul Michael Garrett New police management, performance and accountability, Beverly Metcalf. Hydra-Headed New Public Management: The Case of the National Health Service: Dilemmas beyond the glass ceiling. : the performances of senior women managers in the National Health Service, Alison Linstead and Geraldine Catlow Can the public sector learn? the importation of 'Patient-Focused Care' in an NHS hospital trust, Chris Howorth, Frank Mueller and Charles Harvey 'It's a leap of faith, isn't it? ' managers' perceptions of PFI in the NHS, Sally Ruane New forms of 'Out of Hours' care: from collaboration to competitive entrepreneurialism, Catrina Alferoff and Mike Dent. New Public Management as Contested Terrain: The new public management and higher education: a human cost? , Elisabeth Berg, Jim Barry and John Chandler A bit of a laugh: nurses' use of humour as a mode of resistance, Sharon C. Bolton. The Limits of New Public Management: Uses and limitations of performance measurement in the civil service: an assessment of the Singapore and New Zealand experiences, David Seth Jones Making a 'success' out of failure: darker reflections on private and public management, Tony Cutler Index.
Epigenetics and locust life phase transitions

Insects are one of the most successful classes on Earth, reflected in an enormous species richness and diversity. Arguably, this success is partly due to the high degree to which polyphenism, where one genotype gives rise to more than one phenotype, is exploited by many of its species. In social insects, for instance, larval diet influences the development into distinct castes; and locust polyphenism has tricked researchers for years into believing that the drastically different solitarious and gregarious phases might be different species. Solitarious locusts behave much as common grasshoppers. However, they are notorious for forming vast, devastating swarms upon crowding. These gregarious animals are shorter lived, less fecund and transmit their phase characteristics to their offspring. The behavioural gregarisation occurs within hours, yet the full display of gregarious characters takes several generations, as does the reversal to the solitarious phase. Hormones, neuropeptides and neurotransmitters influence some of the phase traits; however, none of the suggested mechanisms can account for all the observed differences, notably imprinting effects on longevity and fecundity. This is why, more recently, epigenetics has caught the interest of the polyphenism field. Accumulating evidence points towards a role for epigenetic regulation in locust phase polyphenism. This is corroborated in the economically important locust species Locusta migratoria and Schistocerca gregaria. Here, we review the key elements involved in phase transition in locusts and possible epigenetic regulation. We discuss the relative role of DNA methylation, histone modification and small RNA molecules, and suggest future research directions.
Analysis of Joint Provision of Public Goods in Online Communities

Online community (OC, or termed as "virtual community") provides a social sphere for people to share their information, knowledge and other resources. It is becoming an unprecedentedly ubiquitous online phenomenon. The contents which are jointly provided by participants are considered as public goods (Kollock, 1999). For public goods provided by collective action, there have been many papers since Olson (1965) and Hardin (1968). The major concern and conclusion are that enough public goods cannot be provided by rational individuals in collective action. This argument is also applicable to OC because OC will collapse if everyone shirks and free rides others. In the attention economy, however, information overloading becomes a major concern as well, and in response many search and recommendation technologies and services were developed in the Internet including OC. In this case, it seems that "too much" rather than "not enough" public goods are provided in OC. Surprisingly, phenomenon indicates that both "not enough" and "too much" are possible, which contradicts the conclusion of traditional literatures. Hence, this study aims to address why both possibilities exist in OC. How are different results realized by interaction behaviors among participants? Theoretically, we addressed where the optimal level of provision and community size lie. Accordingly, possible managerial strategies are discussed and suggested.
A validation study of the flamelet approach ’ s ability to predict flame structure when fluid mechanics are fully resolved

Modern combustion devices are designed to balance the need for efficient performance with the need for robust performance. Presently available design techniques are capable of meaningfully informing how this balance should be struck. To truly optimize the efficiency and robustness of a combustor, however, the predictive capabilities of numerical simulations will have to be more heavily relied upon. This is because the variables that describe the multi-dimensional combustor design space are related in highly non-linear ways. While empirical numerical models that depict transitions between burned and unburned states are readily available, these models do not provide the level of detail needed for optimizing a combustor’s efficiency. For example, the evolution of important quantities such as CO, NOX, and soot often depend on the details of the time and spatial scales that characterize the structure of the reaction zone. Flamelet approaches are a particular class of combustion model that do capture the time and spatial scales associated with a given asymptotic limit of combustion physics (Peters 2000; Pierce & Moin 2004; Pitsch 2006). This ability to capture the correct limiting physics has historically been viewed as the advantage of the flamelet approach. In modern combustors where mixed-regime behavior is expected, however, the applicability limits of the flamelet approach are not yet well bounded. Single regime non-premixed flamelet implementations, for instance, would not be expected to accurately describe partially premixed or unsteady combustion processes. Furthermore, because the sensitivity of CO, NOX, and soot to predicted reaction zone structure is not fully understood, the accuracy with which singleor multi-regime flamelet approaches predict pollutants in realistic combustors is not known. Therefore it is not currently possible to perform the kind of cost and benefit analysis that is important in selecting an appropriate combustion model for a given application. The objective of this study is to analyze how accurately current flamelet approaches describe complex reaction zone structure in a fully resolved, multi-regime, multi-dimensional laminar flame. Two questions will be used to target this objective. First, how well do single regime (non-premixed) flamelet approaches simulate the detailed flame structure and pollutant signature? Second, do recently developed implementations of multi-regime flamelet methods capture flame structures in any more detail? These questions will be answered by using the flamelet approach to model an unsteady laminar triple flame that has been simulated using a finite rate chemical mechanism for n-heptane.
Tropospheric aerosol impacts on trace gas budgets through photolysis

[1] Aerosols affect the global budgets of O3, OH, and CH4 in part through their alteration of photolysis rates and in part through their direct chemical interactions with gases (i.e., “heterogeneous chemistry”). The first effect is evaluated here with a global tropospheric chemistry transport model using recently developed global climatologies of tropospheric aerosols: a satellite-derived aerosol climatology over the oceans by advanced very high resolution radiometer and a model-generated climatology for land plus oceans by the Center for Climate System Research. Globally averaged, the impact of aerosols on photolysis alone is to increase tropospheric O3 by 0.63 Dobson units and increase tropospheric CH4 by 130 ppb (via tropospheric OH decreases of 8%). These greenhouse gas increases lead to an aerosol indirect effect (counting both natural and anthropogenic aerosols) of +0.08 W/m2. Although the CH4 increases are, of course, global, the changes in tropospheric OH and O3 are mainly regional, with the largest impacts in northwest Africa for January and in India and southern Africa for July. The influence of aerosols is greater in July than in January and greater in the Northern Hemisphere than in the Southern Hemisphere, as expected given the pollution sources in the Northern Hemisphere. The predominant impact is due to the aerosols over land; aerosols over the ocean contribute less than a third to globally integrated changes.
Humor: The Psychology of Living Buoyantly

Preface and Acknowledgements. 1. The changing concerns of psychology. 2. The experiencing of humor in everyday life. 3. Early Conceptions of Humor in Religion, Medicine, Philosophy, and Psychology. 4. The Pervasiveness of Humor. 5. The Many Faces of Humor: Variations in the Types and Definitions of Humor. 6. The Development of Humor: Accounting for Individual Differences in Humor. 7. The Effects of Stress Upon Emotion and Health. 8. Humor as an Emotion-Focused Coping Strategy. 9. Humor as a Means of Retaining Social Cohesion and Support. 10. Sense of Humor and Physiological Stress Responses. 11. Sex and Humor: Interactive Predictors of Health? 12. Summing Up. Appendices. References. Author Index. Subject Index.
Victim Migration: Dynamically Adapting Between Private and Shared CMP Caches

Abstract : Future CMPs will have more cores and greater onchip cache capacity. The on-chip cache can either be divided into separate private L2 caches for each core, or treated as a large shared L2 cache. Private caches provide low hit latency but low capacity, while shared caches have higher hit latencies but greater capacity. Victim replication was previously introduced as a way of reducing the average hit latency of a shared cache by allowing a processor to make a replica of a primary cache victim in its local slice of the global L2 cache. Although victim replication performs well on multithreaded and single-threaded codes, it performs worse than the private scheme for multiprogrammed workloads where there is little sharing between the different programs running at the same time. In this paper, we propose victim migration, which improves on victim replication by adding an additional set of migration tags on each node which are used to implement an exclusive cache policy for replicas. When a replica has been created on a remote node, it is not also cached on the home node, but only recorded in the migration tags. This frees up space on the home node to store shared global lines or replicas for the local processor. We show that victim migration performs better than private, shared, and victim replication schemes across a range of single threaded, multithreaded, and multiprogrammed workloads, while using less area than a private cache design. Victim migration provides a reduction in average memory access latency of up to 10% over victim replication.
Correction: The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

There is an error in the last paragraph of the subsection ‘CDF2 interacts with DCL1’ in the Results and Discussion. “The results showed that the C-terminal fragments of CDF2 interacted with DCL1 as strongly as the full-length CDF2 (Fig 1D),” should read “The results showed that the C-terminal fragments of CDF2 interacted with DCL1 as strongly as the full-length CDF2 (Fig 1E). ” There is an error in the caption for Fig 3. “(B) ChIP-PCR analysis of five promoter fragments of miRNA genes,” should read “(B) ChIP-PCR analysis of six promoter fragments of miRNA genes”. Please see the complete, correct Fig 3 caption here.
Frontoparietal Activation Distinguishes Face and Space from Artifact Concepts

Empirical and theoretical studies suggest that human knowledge is partly based on innate concepts that are experience-independent. We can, therefore, consider concepts underlying our knowledge as being broadly divided into inherited and acquired ones. Using fMRI, we studied the brain reaction in 20 subjects to violation of face, space (inherited), and artifact (acquired) concepts by presenting them with deformed faces, impossible figures (i.e., impossible chairs), and deformed planes, respectively, as well as their normal counterparts. Violation of the inherited concepts of face and space led to significant activation in frontoparietal cortex, whereas artifacts did not, thus distinguishing neurologically between the two categories. Participants were further exposed to these deformities daily for 1 month to test the supposition that inherited concepts are not modifiable, hence that prolonged exposure would not change the brain circuits that are engaged when viewing them. Consistent with this supposition, our results showed no significant change in activation for both categories, suggesting that such concepts are stable at the neural level at least within a time frame of 1 month. Finally, we investigated the regions of the brain that are critical for object representation. Our results show distinct and overlapping areas in the ventral visual cortex for all three categories, with faces activating the ventral visual cortex inferiorly, especially centered on right fusiform gyrus, and chairs and planes activating more diffuse regions, overlapping with the superior part of face region and mainly located in middle occipital cortex and parietal areas.