Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of the weighted histogram method for calculating the thermodynamic parameters of the formation of oligodeoxyribonucleotide duplexes

To date, many derivatives and analogs of nucleic acids (NAs) have been developed. Some of them have found uses in scientific research and biomedical applications. Their effective use is based on the data about their properties. Some of the most important physicochemical properties of oligonucleotides are thermodynamic parameters of the formation of their duplexes with DNA and RNA. These parameters can be calculated only for a few NA derivatives: locked NAs, bridged oligonucleotides, and peptide NAs. Existing predictive approaches are based on an analysis of experimental data and the consequent construction of predictive models. The ongoing pilot studies aimed at devising methods for predicting the properties of NAs by computational modeling techniques are based only on knowledge about the structure of oligonucleotides. In this work, we studied the applicability of the weighted histogram analysis method (WHAM) in combination with umbrella sampling to the calculation of thermodynamic parameters of DNA duplex formation (changes in enthalpy ΔH°, entropy ΔS°, and Gibbs free energy ΔG° 37). A procedure was designed involving WHAM for calculating the hybridization properties of oligodeoxyribonucleotides. Optimal parameters for modeling and calculation of thermodynamic parameters were determined. The feasibility of calculation of ΔH°, ΔS°, and ΔG° 37 was demonstrated using a representative sample of 21 oligonucleotides 4–16 nucleotides long with a GC content of 14–100 %. Error of the calculation of the thermodynamic parameters was 11.4, 12.9, and 11.8 % for ΔH°, ΔS°, and ΔG° 37, respectively, and the melting temperature was predicted with an average error of 5.5 °C. Such high accuracy of computations is comparable with the accuracy of the experimental approach and of other methods for calculating the energy of NA duplex formation. In this paper, the use of WHAM for computation of the energy of DNA duplex formation was systematically investigated for the first time. Our results show that a reliable calculation of the hybridization parameters of new NA derivatives is possible, including derivatives not yet synthesized. This work opens up new horizons for a rational design of constructs based on NAs for solving problems in biomedicine and biotechnology.
ChIP-GPT: a managed large language model for robust data extraction from biomedical database records

Abstract Increasing volumes of biomedical data are amassing in databases. Large-scale analyses of these data have wide-ranging applications in biology and medicine. Such analyses require tools to characterize and process entries at scale. However, existing tools, mainly centered on extracting predefined fields, often fail to comprehensively process database entries or correct evident errors—a task humans can easily perform. These tools also lack the ability to reason like domain experts, hindering their robustness and analytical depth. Recent advances with large language models (LLMs) provide a fundamentally new way to query databases. But while a tool such as ChatGPT is adept at answering questions about manually input records, challenges arise when scaling up this process. First, interactions with the LLM need to be automated. Second, limitations on input length may require a record pruning or summarization pre-processing step. Third, to behave reliably as desired, the LLM needs either well-designed, short, ‘few-shot’ examples, or fine-tuning based on a larger set of well-curated examples. Here, we report ChIP-GPT, based on fine-tuning of the generative pre-trained transformer (GPT) model Llama and on a program prompting the model iteratively and handling its generation of answer text. This model is designed to extract metadata from the Sequence Read Archive, emphasizing the identification of chromatin immunoprecipitation (ChIP) targets and cell lines. When trained with 100 examples, ChIP-GPT demonstrates 90–94% accuracy. Notably, it can seamlessly extract data from records with typos or absent field labels. Our proposed method is easily adaptable to customized questions and different databases.
Associations Between Personality Traits and Adherence to Antidepressants Assessed Through Self-Report, Electronic Monitoring, and Pharmacy Dispensing Data: A Pilot Study

Abstract Treatment with antidepressants is often compromised by substantial nonadherence. To understand nonadherence, specific medication-related behaviors and beliefs have been studied, but less is known about broader and temporally stable personality “traits. ” Furthermore, adherence has often been assessed by a single method. Hence, we investigated associations between the Big Five personality traits and adherence assessed by self-report, electronic drug use monitoring, and dispensing data. Using the Big Five Inventory, we assessed the personality traits “openness,” “conscientiousness,” “extraversion,” “agreeableness,” and “neuroticism” of patients treated with antidepressants who were invited through community pharmacies. Self-reported adherence was assessed with the Medication Adherence Rating Scale (score >24), electronic monitoring with medication event monitoring system (MEMS) devices (therapy days missed ⩽ 10% and < 4 consecutive days missed), and dispensing data (medication possession ratio ≥ 80%). One hundred four women and 33 men participated (mean age, 51; standard deviation, 14). Paroxetine was most frequently prescribed (N = 53, 38%). Logistic regression analysis revealed that of the personality traits, the third and fourth quartiles of “conscientiousness” were associated with better self-reported adherence (odds ratio, 3.63; 95% confidence interval, 1.34–9.86 and odds ratio, 2.97; 95% confidence interval, 1.09–8.08; P ⩽ 0.05). No relationships were found between personality traits and adherence assessed through electronic drug use monitoring or dispensing data. We therefore conclude that adherence to antidepressant therapy seems to be largely unrelated to personality traits.
Research Showcase @ CMU

We consider a statistical database in which a trusted administrator introduces noise to the query responses with the goal of maintaining privacy of individual database entries. In such a database, a query consists of a pair ( S, f ) where S is a set of rows in the database and f is a function mapping database rows to { 0 , 1 } . The true response is (cid:1) r ∈ S f ( DB r ), a noisy version of which is released. Results of Dinur, Dwork, and Nissim show that a strong form of privacy can be maintained using a surprisingly small amount of noise – much less than the sampling error – provided the total number of queries is sublinear in the number of database rows. We call this query and (slightly) noisy reply the SuLQ (Sub-Linear Queries) primitive. The assumption of sublinearity becomes reasonable as databases grow increasingly large. We extend this work in two ways. First, we modify the privacy analysis to real-valued functions f . Second, we examine the computational power of the SuLQ primitive. We show that it is very powerful indeed, in that slightly noisy versons of the following computations can be carried out with very few invocations of the primitive: principal component analysis, k means clustering, the ID3 algorithm, the perceptron algorithm, and (apparently! ) all algorithms in the statistical queries learning model.
Anther development: basic principles and practical applications.

Male reproductive processes in flowering plants take place in the stamen (Esau, 1977). This sporophytic organ system contains diploid cells that undergo meiosis and produce haploid male spores, or microspores. Microspores divide mitotically and differentiate into multicellular male gametophytes, or pollen grains, that contain the sperm cells. Figures 1 and 2 show that the stamen consists of two morphologically distinct partsthe anther and the filament. The filament is a tube of vascular tissue that anchors the stamen to the flower and serves as a conduit for water and nutrients. By contrast, the anther contains the reproductive and nonreproductive tissues that are responsible for producing and releasing pollen grains so that pollination and fertilization processes can occur within the flower. Figure 1 shows that anther development can be divided into two general phases. During phase 1, the morphology of the anther is established, cell and tissue differentiation occur, and microspore mother cells undergo meiosis. At the end of phase 1, the anther contains most of its specialized cells and tissues, and tetrads of microspores are present within the pollen sacs (Figure 1). During phase 2, pollen grains differentiate, the anther enlarges and is pushed upward in the flower by filament extension, and tissue degeneration, dehiscence, and pollen grain release occur (Figure 1). The cellular processes that regulate anther cell differentiation, establish anther tissue patterns, and cause the anther to switch from a histospecification program (phase l) to a cell degeneration and dehiscence program (phase 2) are not known. The developmental events leading to anther formation and pollen release are exquisitely timed and choreographed (Koltunow et al., 1990; Scott et al., 1991). Cell differentiation and dehiscence events occur in a precise chronological order that correlates with floral bud size (Koltunow et al., 1990; Scott et al., 1991). This permits the mechanisms responsible for cell-type differentiation, tissue degeneration, and cellspecific gene activation within the anther to be explored with relative Base. During the past few years, there has been an explosive burst of interest in anther biology, both as a system to dissect plant developmental processes at the molecular and genetic levels (Koltunow et al., 1990; Gasser, 1991; McCormick,
Dense Footprint Cache: Capacity-Efficient Die-Stacked DRAM Last Level Cache

Die-stacked DRAM technology enables a large Last Level Cache (LLC) that provides high bandwidth data access to the processor. However, it requires a large tag array that may take a significant portion of the on-chip SRAM budget. To reduce this SRAM overhead, systems like Intel Haswell relies on a large block (Mblock) size. One drawback of a large Mblock size is that many bytes of an Mblock are not needed by the processor but are fetched into the cache. A recent technique (Footprint cache) to solve this problem works by dividing the Mblock into smaller blocks where only blocks predicted to be needed by the processor are brought into the LLC. While it helps to alleviate the excessive bandwidth consumption from fetching unneeded blocks, the capacity waste remains: only blocks that are predicted useful are fetched and allocated, and the remaining area of the Mblock is left empty, creating holes. Unfortunately, holes create significant capacity overheads which could have been used for useful data, hence wasted refresh power on useless data. In this paper, we propose a new design, Dense Footprint Cache (DFC). Similar to Footprint cache, DFC uses a large Mblock and relies on useful block prediction in order to reduce memory bandwidth consumption. However, when blocks of an Mblock are fetched, the blocks are placed contiguously in the cache, thereby eliminating holes, increasing capacity and power efficiency, and increasing performance. Mblocks in DFC have variable sizes and a cache set has a variable associativity, hence it presents new challenges in designing its management policies (placement, replacement, and update). Through simulation of Big Data applications, we show that DFC reduces LLC miss ratios by about 43%, speeds up applications by 9.5%, while consuming 4.3% less energy on average.
Application of Genotyping during an Extensive Outbreak of Waterborne Giardiasis in Bergen, Norway, during Autumn and Winter 2004

ABSTRACT During the autumn and winter of 2004 and 2005, an extensive outbreak of waterborne giardiasis occurred in Bergen, Norway. Over 1,500 patients were diagnosed with giardiasis. Analysis of water from the implicated source revealed low numbers of Giardia cysts, but the initial contamination event probably occurred up to 10 weeks previously. While sewage leakage from a residential area is now considered to be the probable source of contamination, during the episode waste from one particular septic tank was thought to be a possible source. Genotyping of cysts from the septic tank demonstrated that they were assemblage A cysts, although the sequences were not identical to any previously published sequences. For the β-giardin gene, the closest published subgenotype was subgenotype A3; for the gdh gene, the closest published subgenotype was subgenotype A2. Genotyping of cysts from 21 patient samples revealed that they were assemblage B cysts; thus, the septic tank was unlikely to be the contamination source. Sequencing of the β-giardin and gdh genes from patient samples and a comparison of the sequences gave complex results. For the β-giardin gene, three isolates had sequences identical to subgenotype B3 sequences. However, other isolates had between one and four single-nucleotide polymorphisms (SNPs). For the gdh gene, none of the sequences were identical to the sequence published for subgenotype B3, and the sequences had between one and three SNPs. One isolate, which was identical to subgenotype B3 at the β-giardin gene, was more similar to subgenotype B2 at the gdh gene. Grouping the isolates on the basis of SNPs resulted in different groups for the two genes. The results are discussed in relation to giardiasis in Norway and to other Giardia genotyping studies.
CHICKEN PRODUCTION IN RELATION TO ANIMAL WELFARE AND DISEASE

During the last 20-40 years, there has been a major change in the chickens kept for meat production. The rate of increase in body weight during growth is several times faster than it formerly was but the development of the legs and some physiological systems have changed much less. The conclusion of a European Union (EU) Scientific Report was that “the major welfare problems in broilers are those which can be regarded as side effects of the intense selection mainly for growth and feed conversion. These include leg disorders, ascites, sudden death syndrome in growing birds and welfare problems in breeding birds such as severe food restriction”. A consequence of leg weakness is that the birds crouch down on the litter and may develop dermatitis evident as hock-burn and breast blisters. These painful conditions are quantifiable in chicken carcasses. One way to address this problem is to change genetic selection criteria to slow growth. Another is to increase space allowance and to stimulate locomotion by having sufficient light and a more complex environment. Injury, walking disability and mortality rates can be monitored so that welfare can be improved. By this means, farms can be checked and payment linked to good welfare.
Disrupting the cultural capital of brogrammers

THE PREDOMINANTLY MALE CULTURE poses serious concerns for women in the technology workplace and is a phenomenon that we as instructors of future generations of computer scientists can and should do something about. In his Turing award lecture in 1972 Dijkstra, pleading about how the conceptual importance of problems should override the debates over features of programming languages (“Can you code this in less symbols? ”), was making the case to approach the programming task as one of tremendous difficulty and to respect the intrinsic limitations of the human mind and, therefore, aspire to be humble programmers [1]. It seems that, in the past three decades, not only have we lost sight of these forewarnings but seemed to have crept into the evolution of the so called brogrammer phenomenon [2,3,4,10]. It is the arrogance of the modern day programmer satirically recognized in the tech industry as a person who embodies technical prowess combined with machoness stereotyped in frat-boy behavior and other despicable attributes that are further amplified by the drive to become rich fast (see insert). It is the attitude commonly found in small technology startups and has been depicted in several recent mainstream movies (e.g., The Social Network, The Internship), television shows (e.g., HBO’s Silicon Valley, Amazon.com’s Betas), and written about in popular media. One description is provided by Gavin Belson (played by Matt Ross) in HBO’s Silicon Valley, Episode 1 (2014).
1 . 1 A Shift in Focus

Millions of species currently exist on earth, and to secure an understanding of how all this magnificent variety arose is no small task. Biologists have long accepted Darwinian selection as the central explanation of adaptation and evolutionary change; yet, to date, no similar agreement has emerged about evolutionary processes that can create two species out of one. Almost 150 years after Darwin’s seminal work On the Origin of Species (1859), conditions for and mechanisms of biological speciation are still debated vigorously. The traditional “standard model” of speciation rests on the assumption of geographic isolation. After a population has become subdivided by external causes – like fragmentation through environmental change or colonization of a new, disconnected habitat – and after the resultant subpopulations have remained separated for sufficiently long, genetic drift and pleiotropic effects of local adaptation are supposed to lead to partial reproductive incompatibility. When the two incipient species come into secondary contact, individuals from one species cannot mate with those of the other – even if they try – or, if mating is still possible, their hybrid offspring are inferior. Further evolution of premating isolation (like assortative mate choice or seasonal isolation) and/or postmating isolation (like gametic incompatibility) eventually ensures that the two species continue to steer separate evolutionary courses. The trigger for speciation in this standard model is geographic isolation. It is for this reason that the distinction between allopatric speciation (occurring under geographic isolation) and sympatric speciation (without geographic isolation) has taken center stage in the speciation debate. Strictly speaking, this dichotomy characterizes no more than the spatial structure of populations that undergo speciation, as has been pointed out by the originator of the classification, Ernst Mayr:
Learning Verb Syntax via Listening: New Evidence From 22-Month-Olds

Children recruit verb syntax to guide verb interpretation. We asked whether 22-month-olds spontaneously encode information about a particular novel verb’s syntactic properties through listening to sentences, retain this information in long-term memory over a filled delay, and retrieve it to guide interpretation upon hearing the same novel verb again. Children watched dialogues in which interlocutors discussed unseen events using a novel verb in transitive (e.g., “Anna blicked the baby”) or intransitive sentences (“Anna blicked”). Children later heard the verb in isolation (“Find blicking! ”) while viewing a two-participant causal action and a one-participant action event. Children who had heard transitive dialogues looked longer at the two-participant event than did those who heard intransitive dialogues. This effect disappeared if children heard a different novel verb at test (“Find kradding! ”). These findings implicate a role for distributional learning in early verb learning: syntactic-combinatorial information about otherwise unknown words may pervade the toddler’s lexicon, guiding later word interpretation.
Size-adaptive hepatocellular carcinoma detection from 3D CT images based on the level set method

Automatic detection of hepatocellular carcinoma (HCC) from 3D CT images effectively reduces interpretation work. Several detection methods have been proposed. However, there still remains a tough problem of adaptation detection methods to a wide range of tumor sizes, especially to small nodules, since it is difficult to distinguish tumors from other structures, including noise. Although the level set method (LS) is a powerful tool for detecting objects with arbitrary topology, it is still poor at detecting small nodules due to low contrast. To detect small nodules, early phase images are useful since low contrast in the late phase causes miss-detection of some small nodules. Nevertheless, conventional methods using early phase images face two problems: one is failure to extract small nodules due to low contrast even in early phase images, and the other is false-positive (FP) detection of vessels adjacent to tumors. In this paper, a new robust detection method adapted to the wide range of tumor sizes has been proposed that uses only early phase images. To overcome these two problems, our method consists of two techniques. One is regularizing surface evolution used in LS by applying a new HCC filter that can enhance both small nodules and large tumors. The other is regularizing the surface evolution by applying a Hessian-matrix-based filter that can enhance the vessel structures. Experimental results showed that the proposed method improves sensitivity by over 15% and decreases FP by over 20%, demonstrating that the proposed method is useful for detecting HCC accurately.
Hydrothermal Infilling of a Unique, Layered Spherule Within the Martian Polymict Breccia Northwest Africa 7475

Introduction: The ancient martian polymict breccia Northwest Africa (NWA) 7475 and its paired meteorites [1-3], contain large (mm-sized) vitrophyric spherules [3-5]. These spherules formed by impact melting of hydrothermally altered and weathered rocks of basaltic composition, some or all of the target rocks being sediments [6-7]. All the spherules have fractures in their cores that appear to be cooling and contraction features. In some of the spherules, these fractures are filled with albite-hyalophane (K, Ba-feldspar)magnetite-sulfide veins [5]. A unique, 4.5 mm layered spherule was described by [3] from NWA 7475. This spherule contains numerous smaller minispherules that were described as “captured, glassy spherules” inferred to have been accreted to the large spherule [3]. This unique spherule was studied thoroughly at the Zircon & Accessory Phases Laboratory (ZAP Lab) at Western University, and has been nicknamed ZAP1. In a LAICP-MS study of numerous spherules from the breccia [6-7], it seemed desirable to include ZAP1 since the minispherules within it could provide more detailed information about processes in the impact plumes that formed these spherules. In this study, we report detailed chemical studies by LA-ICP-MS of the complex, layered spherule ZAP1 from NWA 7475 and provide critical data towards a different interpretation of the origin of the mini-spherules as hydrothermal infilling similar to the veins described by [5]. Samples and Analytical Methodology: A chemical map of polished slab NWA 7475 was imaged by SEM-BSE and EDS. When one’s world is limited to a single spherule, one’s thoughts turn cosmological. Accordingly, we named the various mini-spherules within ZAP1 after the characters of the popular TV series, The Big Bang Theory. LA-ICP-MS using an ESITM New WaveTM UP193FX laser ablation system coupled to the Thermo Element XRTM at the Plasma Analytical Facility at FSU was performed following methods detailed elsewhere [6-7]. Most hydrothermal infillings were analyzed using lines with 25-50 μm spot sizes. Three mini-spherules were analyzed using spots of 25100 μm spot sizes. All analyses were conducted using 50 Hz laser repetition rate. Results: ZAP1 consists of three compositional zones: an inner Mg-rich core, an Fe-rich mantle with numerous layered Fe-oxides, and a thin Na-rich rim (Fig. 1). Many of the mini-spherules are present in the Fe-rich mantle consistent with accretionary capture (Fig. 1). The largest of the mini-spherules, Sheldon, consisted of a grain of feldspar at the margin, and a mafic core. Some provided analyses of feldspars only perhaps due to how the mini-spherules intersected the plane of the polished section. Others offered a vitrophyric infilling of unique composition described in more detail below.