Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of field-grown transgenic switchgrass carbon inputs on soil organic carbon cycling

Genetic engineering has been used to decrease the lignin content and to change the lignin composition of switchgrass (Panicum virgatum L.) to decrease cell wall recalcitrance to enable more efficient cellulosic biofuel production. Previous greenhouse and field studies showed that downregulation of the gene encoding switchgrass caffeic acid O-methyltransferase (COMT) and overexpression of the switchgrass PvMYB4 (MYB4) gene effectively improved ethanol yield. To understand potential environmental impacts of cultivating these transgenic bioenergy crops in the field, we quantified the effects of field cultivation of transgenic switchgrass on soil organic carbon (SOC) dynamics. Total and active SOC as well as soil respiration were measured in soils grown with two COMT-downregulated transgenic lines (COMT2 and COMT3), three MYB4-overexpressed transgenic lines (L1, L6, and L8), and their corresponding non-transgenic controls. No differences in total SOC, dissolved organic carbon (DOC), and permanganate oxidizable carbon (POXC) were detected between transgenic and non-transgenic treatments for both COMT (10.4–11.1 g kg−1 for SOC, 60.0–64.8 mg kg−1 for DOC, and 299–384 mg kg−1 for POXC) and MYB4 lines (6.89–8.21 g kg−1 for SOC, 56.0–61.1 mg kg−1 for DOC, and 177–199 mg kg−1 for POXC). Soil CO2-carbon (CO2-C) production from the COMT2 transgenic line was not significantly different from its non-transgenic control. In contrast, the COMT3 transgenic line had greater soil CO2-C production than its non-transgenic control (210 vs. 165 µg g−1) after 72 days of laboratory incubation. Combining the improvement in ethanol yield and biomass production reported in previous studies with negligible change in SOC and soil respiration, COMT2 could be a better biofuel feedstock than COMT3 for environmental conservation and cost-effective biofuel production. On the other hand, MYB4 transgenic line L8 produced more biomass and total ethanol per hectare while it released more CO2-C than the control (253 vs. 207 µg g−1). Long-term in situ monitoring of transgenic switchgrass systems using a suite of soil and environmental variables is needed to determine the sustainability of growing genetically modified bioenergy crops.
lncRNA-SNHG15 accelerates the development of hepatocellular carcinoma by targeting miR-490-3p/ histone deacetylase 2 axis

BACKGROUND Hepatocellular carcinoma (HCC) has become a great threat for people’s health. Many long noncoding RNAs are involved in the pathogenesis of HCC. SNHG15, as a tissue specific long noncoding RNAs, has been studied in many human cancers, except HCC. AIM To explore the regulatory mechanism of SNHG15 in HCC. METHODS In the present research, 101 HCC patient samples, two HCC cell lines and one normal liver cell line were used. RT-qPCR and Western blot analysis were applied to detect SNHG15, miR-490-3p and histone deacetylase 2 (HDAC2) expression. The regulatory mechanism of SNHG15 was investigated using CCK-8, Transwell and luciferase reporter assays. RESULTS Our research showed that up-regulation of SNHG15 was found in HCC and was related to aggressive behaviors in HCC patients. Moreover, knockdown of SNHG15 restrained HCC cell proliferation, migration and invasion. In addition, SNHG15 served as a molecular sponge for miR-490-3p. Further, miR-490-3p directly targets HDAC2. HDAC2 was involved in HCC progression by interacting with the SNHG15/miR-490-3p axis. CONCLUSION In conclusion, long noncoding RNA SNHG15 promotes HCC progression by mediating the miR-490-3p/HDAC2 axis in HCC.
Fidelity of Implementation of Prospera Digital: Evaluation of a Multi-Site mHealth Intervention Aimed at Improving Maternal Health Outcomes in Mexico

ABSTRACT Background Infrastructure and human capital limitations motivate the design of mHealth programs, but their large-scale implementation may be challenging in a development context. Prospera Digital (PD) is a pilot mHealth intervention aiming to improve maternal and child health and nutrition designed as a randomized controlled trial with 3 treatment arms. It was implemented during 2015–2017 in 326 treatment clinics located in 5 states in Mexico. Objective Assess, with an external evaluation, PD's fidelity of implementation using 6 dimensions: adherence, quality, responsiveness, intervention complexity, facilitation strategies, and program differentiation. Methods Benchmark for implementation was first established by interviewing PD's developers. Extensive fieldwork in the 5 states was then conducted to assess its fidelity in heterogeneous contexts. The evaluation team visited 39 health clinics to assess the initial sign-up events and conduct a follow-up. Overall, the team made 28 closed observations; conducted 17 focus groups; and interviewed 74 health providers, 10 community leaders, and 92 beneficiaries. Field notes from the implementation team on all clinics were also examined. Results Co-ordination between the Health and Social Development ministries was adequate, although some health providers were not informed about PD. Program developers added useful implementation strategies during roll-out to reinforce sign-up events. Key quality facilitators were the clarity and relevance of the messages from the short messages service. Beneficiaries expressed high satisfaction with PD. In contrast, implementation barriers to adherence in some localities might reduce the potential impact of PD. Program differentiation was low between the 3 treatment arms. Conclusions PD is a promising strategy to contribute to the promotion of early childhood development in Mexico. Implementation science evaluation can help improve the quality of large-scale mHealth interventions by anticipating barriers and providing insights on how to increase performance. This is especially relevant to inform impact evaluation in development contexts. The trial was registered at the American Economic Association's registry for randomized controlled trials with trial registry number ‘AEARCTR-0001035’.
Real-time reverse transcription polymerase chain reaction development for rapid detection of Tomato brown rugose fruit virus and comparison with other techniques

Background Tomato brown rugose fruit virus (ToBRFV) is a highly infectious tobamovirus that causes severe disease in tomato (Solanum lycopersicum L.) crops. In Italy, the first ToBRFV outbreak occurred in 2018 in several provinces of the Sicily region. ToBRFV outbreak represents a serious threat for tomato crops in Italy and the Mediterranean Basin. Methods Molecular and biological characterisation of the Sicilian ToBRFV ToB-SIC01/19 isolate was performed, and a sensitive and specific Real-time RT-PCR TaqMan minor groove binder probe method was developed to detect ToBRFV in infected plants and seeds. Moreover, four different sample preparation procedures (immunocapture, total RNA extraction, direct crude extract and leaf-disk crude extract) were evaluated. Results The Sicilian isolate ToB-SIC01/19 (6,391 nt) showed a strong sequence identity with the isolates TBRFV-P12-3H and TBRFV-P12-3G from Germany, Tom1-Jo from Jordan and TBRFV-IL from Israel. The ToB-SIC01/19 isolate was successfully transmitted by mechanical inoculations in S. lycopersicum L. and Capsicum annuum L. , but no transmission occurred in S. melongena L. The developed real-time RT-PCR, based on the use of a primer set designed on conserved sequences in the open reading frames3, enabled a reliable quantitative detection. This method allowed clear discrimination of ToBRFV from other viruses belonging to the genus Tobamovirus, minimising false-negative results. Using immunocapture and total RNA extraction procedures, the real-time RT-PCR and end-point RT-PCR gave the same comparable results. Using direct crude extracts and leaf-disk crude extracts, the end-point RT-PCR was unable to provide a reliable result. This developed highly specific and sensitive real-time RT-PCR assay will be a particularly valuable tool for early ToBRFV diagnosis, optimising procedures in terms of costs and time.
Pertuzumab and Trastuzumab Emtansine for Human Epidermal Growth Factor Receptor-2–Positive Metastatic Breast Cancer: Contemporary Population-Based Outcomes

Background: Real-world outcomes for patients with human epidermal growth factor receptor-2 (HER2)-positive metastatic breast cancer (MBC) treated with pertuzumab in combination with taxane chemotherapy plus trastuzumab (TaxTP) in the first line setting and trastuzumab emtansine (TE) in any line of treatment are lacking. Methods: Cohorts of patients treated with (1) TaxTP and (2) TE from January 1, 2013 through December 31, 2016 were retrospectively obtained from a population-based database. Cohorts were described according to age, hormone receptor (HR) status, prior systemic therapies, event-free survival (EFS) defined as time from start of treatment to start of next line of treatment or death, and overall survival (OS). Results: A total of 122 patients were treated with TaxTP and 104 with TE. In the TaxTP cohort, EFS was significantly longer in the trastuzumab-naïve group compared with the adjuvant trastuzumab group (median EFS = 27.0 vs 12.4 months; P = .002). In the TaxTP cohort, median OS was not reached. In the TE cohort, EFS was significantly longer in the pertuzumab-naïve group compared with pertuzumab-exposed group (median time to treatment failure [TTF] = 18.7 vs 5.5 months; P < .001). Overall survival was also significantly longer in the pertuzumab-naïve group compared with the pertuzumab-exposed group (median OS = 23.2 vs 14.1 months; P = .022). In multivariable analyses, adjuvant trastuzumab and prior pertuzumab exposure in the metastatic setting remained significant predictors of inferior EFS for patients treated with TaxTP and TE, respectively. Conclusions: New anti-HER2 therapies appear to be clinically relevant in the real-world.
Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.
Effects of soil pH and texture on soil carbon and nitrogen in soil profiles under different land uses in Mun River Basin, Northeast Thailand

Soil carbon and nitrogen are essential factors for agricultural production and climate changes. A total of 106 soil samples from three agricultural lands (including two rice fields and one sugarcane field) and four non-agricultural lands (including two forest lands, one wasteland and one built-up land) in the Mun River Basin were collected to determine soil carbon, nitrogen, soil pH, soil particle sizes and explore the influence of pH and soil texture on soil C and N. The results show that total organic carbon (TOC) and nitrogen (TON) contents in topsoil (TOC: 2.78 ~ 18.83 g kg−1; TON: 0.48 ~ 2.05 g kg−1) are much higher than those in deep soil (TOC: 0.35 ~ 6.08 g kg−1; TON: <0.99 g kg−1). In topsoil, their contents of forest lands and croplands (TOC: average 15.37 g kg−1; TON: average 1.29 g kg−1) are higher than those of other land uses (TOC: average 5.28 g kg−1; TON: average 0.38 g kg−1). The pH values range from 4.2 to 6.1 in topsoil, and with increase in soil depth, they tend to increase and then decrease. Soil carbon, nitrogen and the C/N (TC/TN ratio) are negatively correlated with soil pH, demonstrating that relatively low pH benefits the accumulation of organic matter. Most soil samples are considered as sandy loam and silt loam from the percentages of clay, silt and sand. For soil profiles below 50 cm, the TOC and TON average contents of soil samples which contain more clay and silt are higher than those of other soil samples.
Early Surgical Repair of Bile Duct Injuries following Laparoscopic Cholecystectomy: The Sooner the Better

Abstract Background We aimed to investigate the outcomes of the immediate surgical repair of bile duct injuries (BDIs) following laparoscopic cholecystectomy. Materials and Methods Between January 2012 and May 2017, patients, who underwent immediate surgical repair (within 72 hours) for postcholecystectomy BDI, by the same surgical team expert in hepatobiliary surgery, were enrolled into the study. Data collection included demographics, type of BDI according to the Strasberg classification, time to diagnosis, surgical procedures, and outcome. Results There were 13 patients with a mean age of 43 ± 12 years. Classification of BDIs were as follows: type E in six patients (46%), type D in three patients (23%), type C in two (15%), and types B and A in one patient each (7.6%). Mean time to diagnosis was 22 ± 15 hours. Surgical procedures included Roux-en-Y hepaticojejunostomy for all six patients with type-E injury, primary repair of common bile duct for three patients with type-D injury, and primary suturing of the fistula orifice was performed in two cases with type-C injury. Other two patients with type-B and -A injury underwent removal of clips which were placed on common bile duct during index operation and replacing of clips on cystic duct where stump bile leakage was observed probably due to dislodging of clips, respectively. Mean hospital stay was 6.6 ± 3 days. Morbidity with a rate of 30% (n = 4) was observed during a median follow-up period of 35 months (range: 6–56 months). Mortality was nil. Conclusion Immediate surgical repair of postcholecystectomy BDIs in selected patients leads to promising outcome.
Block size analysis for discrete wavelet watermarking and embedding a vector image as a watermark

: As telecommunication and computer technologies proliferate, most data are stored and transferred in digital format. Content owners, therefore, are searching for new technologies to protect copyrighted products in digital form. Image watermarking emerged as a technique for protecting image copyrights. Early studies on image watermarking used the pixel domain whereas modern watermarking methods convert a pixel based image to another domain and embed a watermark in the transform domain. This study aims to use, Block Discrete Wavelet Transform (BDWT) as the transform domain for embedding and extracting watermarks. This study consists of 2 parts. The first part investigates the effect of dividing an image into non-overlapping blocks and transforming each image block to a DWT domain, independently. Then, effect of block size on watermark success and, how it is related to block size, are analyzed. The second part investigates embedding a vector image logo as a watermark. Vector images consist of geometric objects such as lines, circles and splines. Unlike pixel-based images, vector images do not lose quality due to scaling. Vector watermarks deteriorate very easily if the watermarked image is processed, such as compression or filtering. Special care must be taken when the embedded watermark is a vector image, such as adjusting the watermark strength or distributing the watermark data into the image. The relative importance of watermark data must be taken into account. To the best of our knowledge this study is the first to use a vector image as a watermark embedded in a host image .
Gel-based Haptic Mediator for High-Definition Tactile Communication

In an effort to find a way to more efficiently and accurately display localized high definition tactile information to the skin we studied the vibrotactile constructive wave interference properties of silicone gel. By placing two actuators at a given distance from each other and controlling the delay when each actuator is activated in relation to the other, we can achieve a point of constructive wave interference. The time when the interference occurs along with any loses due to attenuation depends on the material the vibration travels through. The goal is to find a compliant material that can be used as a reference to human tissue when designing feedback for assistive robots.
Internet Performance from Facebook's Edge

We examine the current state of user network performance and opportunities to improve it from the vantage point of Facebook, a global content provider. Facebook serves over 2 billion users distributed around the world using a network of PoPs and interconnections spread across 6 continents. In this paper, we execute a large-scale, 10-day measurement study of metrics at the TCP and HTTP layers for production user traffic at all of Facebook's PoPs worldwide, collecting performance measurements for hundreds of trillions of sampled HTTP sessions. We discuss our approach to collecting and analyzing measurements, including a novel approach to characterizing user achievable goodput from the server side. We find that most user sessions have MinRTT less than 39ms and can support HD video. We investigate if it is possible to improve performance by incorporating performance information into Facebook's routing decisions; we find that default routing by Facebook is largely optimal. To our knowledge, our measurement study is the first characterization of user performance on today's Internet from the vantage point of a global content provider.
BubBowl: Display Vessel Using Electrolysis Bubbles in Drinkable Beverages

Research was conducted regarding a display that presents digital information using bubbles. Conventional bubble displays require moving parts, because it is common to use air taken from outside of the water to represent pixels. However, it is difficult to increase the number of pixels at a low cost. We propose a liquid-surface display using pixels of bubble clusters generated from electrolysis, and present the cup-type device BubBowl, which generates a 10×10 pixel dot matrix pattern on the surface of a beverage. Our technique requires neither a gas supply from the outside nor moving parts. Using the proposed electrolysis method, a higher-resolution display can easily be realized using a PCB with a higher density of matrix electrodes.Moreover, the method is simple and practical, and can be utilized in daily life, such as for presenting information using bubbles on the surface of coffee in a cup.
A Longitudinal Analysis of the ads.txt Standard

Programmatic advertising provides digital ad buyers with the convenience of purchasing ad impressions through Real Time Bidding (RTB) auctions. However, programmatic advertising has also given rise to a novel form of ad fraud known as domain spoofing, in which attackers sell counterfeit impressions that claim to be from high-value publishers. To mitigate domain spoofing, the Interactive Advertising Bureau (IAB) Tech Lab introduced the ads.txt standard in May 2017 to help ad buyers verify authorized digital ad sellers, as well as to promote overall transparency in programmatic advertising. In this work, we present a 15-month longitudinal, observational study of the ads.txt standard. We do this to understand (1) if it is helping ad buyers to combat domain spoofing and (2) whether the transparency offered by the standard can provide useful data to researchers and privacy advocates. With respect to halting domain spoofing, we observe that over 60% of Alexa Top-100K publishers that run RTB ads have adopted ads.txt, and that ad exchanges and advertisers appear to be honoring the standard. With respect to transparency, the widespread adoption of ads.txt allows us to explicitly identify over 1,000 domains belonging to ad exchanges, without having to rely on crowdsourcing or heuristic methods. However, we also find that ads.txt is still a long way from reaching its full potential. Many publishers have yet to adopt the standard, and we observe major ad exchanges purchasing unauthorized impressions that violate the standard. This opens the door to domain spoofing attacks. Further, ads.txt data often include errors that must be cleaned and mitigated before the data is practically useful.
What Did I Miss?

In Massive Open Online Courses (MOOCs), learners face a lot of distractions which will cause divided attention (DA). However, it is not easy for learners to realize that they are distracted and to find out which part of the course they have missed. In this paper, we present Reminder, a system for detecting divided attention and reminding learners what they just missed on both PC and mobile devices with a camera capturing their status. To get learners' attention level, we build a regression model to predict attention score from an integrated feature vector. Meanwhile, we design an interactively updating method to make the model adaptive to a specific user. We also propose a visualization method to help learners review missed content easily. User study shows that Reminder detects learners' divided attention and assists them to review missed course contents effectively.
Resized Grasping in VR: Estimating Thresholds for Object Discrimination

Previous work in VR has demonstrated how individual physical objects can represent multiple virtual objects in different locations by redirecting the user's hand. We show how individual objects can represent multiple virtual objects of different sizes by resizing the user's grasp. We redirect the positions of the user's fingers by visual translation gains, inducing an illusion that can make physical objects seem larger or smaller. We present a discrimination experiment to estimate the thresholds of resizing virtual objects from physical objects, without the user reliably noticing a difference. The results show that the size difference is easily detected when a physical object is used to represent an object less than 90% of its size. When physical objects represent larger virtual objects, however, then scaling is tightly coupled to the physical object's size: smaller physical objects allow more virtual resizing (up to a 50% larger virtual size). Resized Grasping considerably broadens the scope of using illusions to provide rich haptic experiences in virtual reality.