Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota

Objective N-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms. Methods After treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways. Results Compared to the control group, the values of Cmax, AUC0-8, AUC0-∞, t1/2 in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmax values decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism. Conclusion Antibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposure in vivo by inhibiting pathways related to NBP metabolism.
Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis

Background As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses. Results We developed Trans2express – a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabidopsis thaliana cDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms. The comparison of structural characteristics of the transcriptome assembly with reference Arabidopsis genome revealed the high quality of assembled transcriptome with 86.1% of Arabidopsis expressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis and showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly. Conclusions We present Trans2express – a protocol for de novo hybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.
Fabrication of Organic Light Emitting Diodes (OLEDs) using the Lamination method in a Vacuum-Free Environment

Organic Light Emitting Diodes (OLEDs) have recently become one of the fastest-growing technologies in the world. The challenge in OLED fabrication, especially larger-area OLEDs, is its relatively high costs and complexity. The lamination method in a vacuum-free environment is an approach to simplify and reduce the cost of fabrication. This paper reports our latest progress on OLEDs fabricated using the said method and condition. The processing parameters were explored and optimized. Spin coating the emissive Layer (PFO) at 1300 rpm and the anode (TC-07-S) at 3000 rpm yield the best results in terms of current conduction and success rate. Laminating the OLEDs at 160 °C, with 245 N of force, and for 30 seconds, gave the best results in terms of previously stated parameters. Furthermore, the constituting materials of the OLEDs were explored. It was found that TC-07-S as an anode, PFO as the light-emitting material, a 30-micrometer thick aluminum foil as the cathode, and Kapton as the dielectric and adhesive material yielded the best results. These results may pave the way for other innovative methods to fabricate OLEDs with simple and affordable processes.
Human inductive biases for aversive continual learning - a hierarchical Bayesian nonparametric model

Humans and animals often display remarkable continual learning abilities, adapting quickly to changing environments while retaining, reusing, and accumulating old knowledge over a lifetime. Unfortunately, in environments with adverse outcomes, the inductive biases supporting such forms of learning can turn maladaptive, yielding persistent negative beliefs that are hard to extinguish, such as those prevalent in anxiety disorders. Here, we present and model human behavioral data from a fear-conditioning task with changing latent contexts, in which participants had to predict whether visual stimuli would be followed by an aversive scream. We show that participants’ learning in our task spans three different regimes — with old knowledge either being updated, discarded (forgotten) or retained and reused in new contexts (remembered) by different participants. The latter regime corresponds to (maladaptive) spontaneous recovery of fear. We demonstrate using simulations that these behavioral regimes can be captured by varying inductive biases in Bayesian non-parametric models of contextual learning. In particular, we show that the “remembering” regime can be produced by “persistent” variants of hierarchical Dirichlet process priors over contexts and negatively biased “deterministic” beta distribution priors over outcomes. Such inductive biases correspond well to widely observed “core beliefs” that may have adaptive value in some lifelong-learning environments, at the cost of being maladaptive in other environments and tasks such as ours. Our work offers a tractable window into human inductive biases for continual learning algorithms, and could potentially help identify individual differences in learning strategies relevant for response to psychotherapy.
The Mediating Role of Information System (IS) Process Between Technology, Organization & Environment and Competitive Advantage in Using Cloud Computing Services (CCS)

In Malaysia, the use of cloud computing services (CCS) has become essential for any kind of organization. An increasing number of organizations are beginning to store, manage, and access their data and apps via the internet by using CCS instead of local servers. In the digital age, CCS helps Malaysian businesses to function more effectively, produce better results, and maintain their competitiveness. The primary objective is to examine the influence of CCS on organizations in Malaysia, emphasizing the crucial interplay between technology, organizational environment, and competitive advantages. Furthermore, the study aims to explore the role of information system (IS) processes as a mediating factor in optimizing CCS to attain competitive advantages among Malaysia Digital (MD) status company. This research seeks to provide insights into the specific case of MD Status company, offering concise, informative, and engaging findings tailored for academic and professional audiences.
Applying Test-Driven Development and Reverse Engineering Patterns to Reengineer Legacy Software Systems

Nowadays, software technology is evolving quickly and therefore software systems which have been built upon some technologies are deprecated even before being released and used. Thus, software systems are in constant evolution in order to adapt themselves to the current technologies as well as users’ needs. An approach to revitalize software systems that have already been released is reengineering. In this paper, we propose an iterative reengineering approach that uses reverse engineering patterns and test-driven development to cope with issues involved in migrating from a legacy system to an equivalent software system implemented in more recent technologies. As a preliminary evaluation of the proposed approach, we contrasted it with an ad-hoc approach during the reengineering of a legacy system from Smalltalk to Java.
Fuzzy Identity Based Encryption with a flexible threshold value

— The issue of data and information security on the internet and social network has become more serious and pervasive in recent years. Cryptography is used to solve security problems. However, message encryption cannot merely meet the intended goals because access control over the encrypted messages is required in some applications. To achieve these requirements, attribute-based encryption (ABE) is used. This type of encryption provides both security and access structure for the network users simultaneously. Fuzzy Identity-Based Encryption (FIBE) is a special mode of ABE that provides a threshold access structure for the users. This threshold value is set by the authority for users, which is always fixed and cannot be changed. So, the sender (encryptor) will not play a role in determining the threshold value. The mentioned issue exists also in
Influence of Land Use Activities on Riparian Vegetation, Soil and Water Quality: An Indicator of Biodiversity Loss, South West Mau Forest, Kenya

Watershed and riparian areas of Mau Forest Complex in Kenya are experiencing increased threats due to unsustainable land use activities geared towards economic growth amidst growing population. This study was carried out to examine effects of land use activities on riparian vegetation, soil and water quality along two major rivers (Chemosit and Kipsonoi) of South West Mau Forest (SWMF). Land use activities adjacent to these rivers and biodiversity disturbance on the riparian zone were identified and underpinned to changes on Total Nitrogen, Total Phosphorous, Potassium, Sulphur, Cadmium, Copper, Lead, Total Suspended Solids and soil Organic Carbon. Three sampling sites designated(upstream, midstream and downstream) were identified and established along each river as guided by existing land use activities represented by forest, tea plantation and mixed agricultural farming respectively. At each sampling site, a 200 m × 50 m section was systematically marked on each side of the river bank; the longest side being parallel to the river flow and divided into three belts transects each 20 m × 50 m, spaced 70 m apart. Six distinct land use activities (indigenous forest, food crop, tree and tea farming, livestock keeping and urban settlement) were identified as the major land use activities in SWMF. Plant species richness decreased and overall riparian disturbance increased from upstream (intact canopy with native vegetation) to mid-stream and downstream as epitomized by the structure, biodiversity disturbance resulting from extensive and intensive farming, intrusion of exotic species to livestock grazing and urban settlement. Variation among sampling sites in Total Suspended Solids, pH, Total Nitrogen, Phosphorus and Potassium were associated to different land use activities along the riparian zone. Total Nitrogen and water pH showed significant sensitivity to land use changes (p < 0.05). Put together these results indicate loss of biodiversity, riparian disturbance hence a need to adopt environmental-friendly land use planning and sustainable farming systems in SWMF.
Testosterone deprivation accelerates cardiac dysfunction in obese male rats 1 2

4 Department of Oral Biology and Diagnostic Science, Faculty of Dentistry, Chiang Mai University, 12 Chiang Mai, Thailand 13 14 Corresponding Author: 15 Nipon Chattipakorn, MD, PhD 16 Cardiac Electrophysiology Research and Training Center, 17 Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand 18 E-mail: nchattip@gmail.com 19 20 Short title: Obese-testosterone deprivation and the heart 21 Key terms: Testosterone deprivation; Obese-insulin resistance; Cardiac Function; Cardiac 22 Mitochondrial function 23 Word count: 5,000 words 24 Page 1 of 33 Accepted Preprint first posted on 21 March 2016 as Manuscript JOE-16-0002
HasTEE+ : Confidential Cloud Computing and Analytics with Haskell

Confidential computing is a security paradigm that enables the protection of confidential code and data in a co-tenanted cloud deployment using specialized hardware isolation units called Trusted Execution Environments (TEEs). By integrating TEEs with a Remote Attestation protocol, confidential computing allows a third party to establish the integrity of an \textit{enclave} hosted within an untrusted cloud. However, TEE solutions, such as Intel SGX and ARM TrustZone, offer low-level C/C++-based toolchains that are susceptible to inherent memory safety vulnerabilities and lack language constructs to monitor explicit and implicit information-flow leaks. Moreover, the toolchains involve complex multi-project hierarchies and the deployment of hand-written attestation protocols for verifying \textit{enclave} integrity. We address the above with HasTEE+, a domain-specific language (DSL) embedded in Haskell that enables programming TEEs in a high-level language with strong type-safety. HasTEE+ assists in multi-tier cloud application development by (1) introducing a \textit{tierless} programming model for expressing distributed client-server interactions as a single program, (2) integrating a general remote-attestation architecture that removes the necessity to write application-specific cross-cutting attestation code, and (3) employing a dynamic information flow control mechanism to prevent explicit as well as implicit data leaks. We demonstrate the practicality of HasTEE+ through a case study on confidential data analytics, presenting a data-sharing pattern applicable to mutually distrustful participants and providing overall performance metrics.
Identifying Symptoms Prior to Pancreatic Ductal Adenocarcinoma Diagnosis in Real-World Care Settings: Natural Language Processing Approach

Background: Pancreatic cancer is the third leading cause of cancer deaths in the United States. Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer, accounting for up to 90% of all cases. Patient-reported symptoms are often the triggers of cancer diagnosis and therefore, understanding the PDAC-associated symptoms and the timing of symptom onset could facilitate early detection of PDAC. Objective: This paper aims to develop a natural language processing (NLP) algorithm to capture symptoms associated with PDAC from clinical notes within a large integrated health care system. Methods: We used unstructured data within 2 years prior to PDAC diagnosis between 2010 and 2019 and among matched patients without PDAC to identify 17 PDAC-related symptoms. Related terms and phrases were first compiled from publicly available resources and then recursively reviewed and enriched with input from clinicians and chart review. A computerized NLP algorithm was iteratively developed and fine-trained via multiple rounds of chart review followed by adjudication. Finally, the developed algorithm was applied to the validation data set to assess performance and to the study implementation notes. Results: A total of 408,147 and 709,789 notes were retrieved from 2611 patients with PDAC and 10,085 matched patients without PDAC, respectively. In descending order, the symptom distribution of the study implementation notes ranged from 4.98% for abdominal or epigastric pain to 0.05% for upper extremity deep vein thrombosis in the PDAC group, and from 1.75% for back pain to 0.01% for pale stool in the non-PDAC group. Validation of the NLP algorithm against adjudicated chart review results of 1000 notes showed that precision ranged from 98.9% (jaundice) to 84% (upper extremity deep vein thrombosis), recall ranged from 98.1% (weight loss) to 82.8% (epigastric bloating), and F 1 -scores ranged from 0.97 (jaundice) to 0.86 (depression). Conclusions: The developed and validated NLP algorithm could be used for the early detection of PDAC.
Correlations between ﬂow and transverse momentum in Xe + Xe and Pb + Pb collisions at the LHC with the ATLAS detector: A probe of the heavy-ion initial state and nuclear deformation

The correlations between ﬂow harmonics v n for n = 2, 3, and 4 and mean transverse momentum [ p T ] in 129 Xe + 129 Xe and 208 Pb + 208 Pb collisions at √ s = 5 . 44 and 5.02 TeV, respectively, are measured using charged particles with the ATLAS detector. The correlations are potentially sensitive to the shape and size of the initial geometry, nuclear deformation, and initial momentum anisotropy. The effects from nonﬂow and centrality ﬂuctuations are minimized, respectively, via a subevent cumulant method and an event-activity selection based on particle production at very forward rapidity. The v n -[ p T ] correlations show strong dependencies on centrality, harmonic number n , p T , and pseudorapidity range. Current models qualitatively describe the overall centrality-and system-dependent trends but fail to quantitatively reproduce all features of the data. In central collisions, where models generally show good agreement, the v 2 -[ p T ] correlations are sensitive to the triaxiality of the quadruple deformation. Comparison of the model with the Pb + Pb and Xe + Xe data conﬁrms that the 129 Xe nucleus is a highly deformed triaxial ellipsoid that has neither a prolate nor oblate shape. This provides strong evidence for a triaxial deformation of the 129 Xe nucleus from high-energy heavy-ion collisions. DOI: 10.1103/PhysRevC.107. 054910
Original Research Barriers to HIV Related Services among Men Who Have Sex with Men (MSM) in Rural Georgia

Background: Gay, bisexual, and men who have sex with men (MSM) living in the Southeastern United States are at high risk of contracting HIV, and those in rural communities experience challenges in accessing HIV prevention and treatment. Methods: Seven healthcare workers and 17 MSM in rural healthcare districts participated in semi-structured interviews. A theory-informed thematic analysis approach was used to summarize and compare perspectives between healthcare workers and MSM participants. Results: Stigma, insufficient resources, and social structures of rural life emerged as barriers to accessing HIV-related services. Conclusions: Overcoming these barriers are necessary to reduce HIV infection and improve outcomes for MSM living with HIV. The findings come at a critical time given the focus on rural areas affected by HIV as announced in United States’ Ending the HIV Epidemic Initiative. Additional resources need to be allocated and research is needed to understand the relationship among rural health, HIV, and MSM.
IPFS in the Fast Lane: Accelerating Record Storage with Optimistic Provide

—The centralization of web services has raised concerns about critical single points of failure, such as content hosting, name resolution, and certification. To address these issues, the “Decentralized Web” movement advocates for de-centralized alternatives. Distributed Hash Tables (DHTs) have emerged as a key component facilitating this movement, as they offer efficient key/value indexing. The InterPlanetary File System (IPFS) exemplifies this approach by leveraging DHTs for data indexing and distribution. A critical finding of previous studies is that DHT PUT performance for record storage is unacceptably slow, sometimes taking minutes to complete and hindering the adoption of delay-intolerant applications. To address this challenge, this research paper presents three significant contributions. First, we present the design of Optimistic Provide, an approach to accelerate DHT PUT operations in Kademlia-based IPFS networks while maintaining full backward compatibility. Second, we implement and deploy the mechanism and see its usage in the de-facto IPFS deployment, Kubo. Third, we evaluate its effectiveness in the IPFS and Filecoin DHTs. We confirm that we enable sub-second record storage from North America and Europe for 90% of PUT operations while reducing networking overhead by over 40% and maintaining record availability.
Cooperation on the Web: trends and practice in the development sector

To deal with the challenges and opportunities posed by the Internet, the authors argue that the information and communication ‘strategies’ of development organisations must be based around notions of cooperation and communities. This paper introduces some information-sharing and management trends on the Internet, exploring the growth in gateways and portals, and briefly profiling several cooperative efforts. Discussion is focused on the institutional dimensions of this cooperation, looking at issues like ownership, participation, sustainability, and ‘cooperativity’. The authors conclude by calling for more joint action in which development organizations, together, seek to harness the power of the Internet.
Eﬀicient and Generalized Decentralized Monitoring of Regular Languages

This paper proposes an efﬁcient and generalized decentralized monitoring algorithm allowing to detect satisfaction or violation of any regular speciﬁ-cation by local monitors alone in a system without central observation point. Our algorithm does not assume any form of synchronization between system events and communication of monitors, uses state machines as underlying mechanism for efﬁciency, and tries to keep the number and size of messages exchanged be-tween monitors to a minimum. We provide a full implementation of the algorithm with an open-source benchmark to evaluate its efﬁciency in terms of number, size of exchanged messages, and delay induced by communication between monitors. Experimental results demonstrate the effectiveness of our algorithm which out-performs the previous most general one along several (new) monitoring metrics.