Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of Plant Production by Seed Treatment in Two Wild Subspecies of Narcissus pseudonarcissus Rich in Alkaloids

The daffodil Narcissus pseudonarcissus L. contains alkaloids of pharmaceutical interest. Wild daffodil populations have diverse genetic backgrounds and various genetic traits of possible importance. Developing protocols for plant production from seeds may ensure the availability of a large reservoir of individuals as well as being important for species with bulbs that are difficult to acquire. The closely related Narcissus pseudonarcissus subsp. munozii-garmendiae and subsp. nevadensis were investigated in this study because the alkaloids isolated from both are of high pharmacological interest. At the dispersal time, the seeds of both were dormant with underdeveloped embryos, i.e., morphophysiological dormancy (MPD). Experiments were conducted outdoors and under controlled laboratory conditions. Embryo growth and the percentages of radicle and seedling emergence were calculated under different temperature–light stratifications. In N. munozii-garmendiae, embryo growth occurred during warm stratification (28/14 °C or 25/10 °C) and the radicle then emerged when the temperature decreased, but the shoot was dormant. In N. nevadensis, the seeds germinated when cold stratified (5 °C) and then incubated at cool temperatures. Thus, N. munozii-garmendiae and N. nevadensis exhibit different levels of MPD, i.e., deep simple epicotyl and intermediate complex, respectively. Plant production protocols from seeds were established for both taxa in this study.
Perceived barriers to paternal expanded carrier screening following a positive maternal result: To screen or not to screen

Expanded carrier screening identifies individuals who are at risk of having a child with an autosomal recessive condition. The most accurate risk assessment requires that both mother and father undergo carrier screening to determine whether they are carriers of the same autosomal recessive condition. A couple identified as carriers of the same condition has a 25% chance of having a child with that condition. However, the father does not always opt for carrier screening following a positive result in the mother. This study aimed to identify barriers that prevent the father from carrier screening after a positive finding in the mother. A total of 58 women participated in this study. All participants had undergone expanded carrier screening prior to the study and had met with a genetic counselor for a pre‐test, informed consent session. Of the 58 women, 34 had partners who did not undergo screening and 24 had partners who did. Participants completed a survey to determine the barriers that prevented the father of the baby's participation. We report that the mother's insurance type, whether the father has insurance, relationship status, and knowledge of the carrier screen showed statistically significant differences between women whose partners underwent screening and those that did not. In summary, our finding suggests that increasing insurance coverage of paternal screening and improving the patient's knowledge of the expanded screen would encourage paternal screening.
Phylogeny and In Silico Structure Analysis of Major Capsid Protein (L1) Human Papillomavirus 45 from Indonesian Isolates

Background: Human papillomavirus (HPV)-45 genotype circulates in high percentage in Bandung area - Indonesia, after HPV-16 and HPV-18. The aim of this study was to analyse variations of major capsid (L1) HPV-45 and its phylogeny. Furthermore in silico protein structure and epitope prediction was explored. Methods: L1 gene of HPV-45 was amplified, sequenced and aligned. Phylogenetic tree had been built and compared with a complete L1 HPV-45 sequence. Structure and epitope prediction of L1 protein were then developed in silico. Results: Of 5 L1 HPV-45 sequences collected, we have detected one variant of sub lineage A2 which was considered as a new variant, and two variants of B2. Superimposition of structure of these two variants with reference showed very similar structure. Furthermore, seven amino acid substitutions were found within these L1 variants of which two substitutions might change the polarity of corresponding amino acid I329T and S383G. The S383G occurred in surface loop (HI-Loop) of new L1 HPV-45 variant. Conclusion: Similar structure of Indonesian variants indicates that amino acids variations do not affect the L1 structure. However, one substitution with altered amino acid polarity found within the area of surface loop suggests a potential impact in antibody recognition and neutralization.
Possible Cross-Reactivity between SARS-CoV-2 Proteins, CRM197 and Proteins in Pneumococcal Vaccines May Protect Against Symptomatic SARS-CoV-2 Disease and Death

Various studies indicate that vaccination, especially with pneumococcal vaccines, protects against symptomatic cases of SARS-CoV-2 infection and death. This paper explores the possibility that pneumococcal vaccines in particular, but perhaps other vaccines as well, contain antigens that might be cross-reactive with SARS-CoV-2 antigens. Comparison of the glycosylation structures of SARS-CoV-2 with the polysaccharide structures of pneumococcal vaccines yielded no obvious similarities. However, while pneumococcal vaccines are primarily composed of capsular polysaccharides, some are conjugated to cross-reacting material CRM197, a modified diphtheria toxin, and all contain about three percent protein contaminants, including the pneumococcal surface proteins PsaA, PspA and probably PspC. All of these proteins have very high degrees of similarity, using very stringent criteria, with several SARS-CoV-2 proteins including the spike protein, membrane protein and replicase 1a. CRM197 is also present in Haemophilus influenzae type b (Hib) and meningitis vaccines. Equivalent similarities were found at lower rates, or were completely absent, among the proteins in diphtheria, tetanus, pertussis, measles, mumps, rubella, and poliovirus vaccines. Notably, PspA and PspC are highly antigenic and new pneumococcal vaccines based on them are currently in human clinical trials so that their effectiveness against SARS-CoV-2 disease is easily testable.
Birth size and growth of deer fawns in southern Illinois

of white-tailed deer fawns. Trans. North Am. Wildl. and Nat. Resour. Conf. 28:481-443. 1965. Reproduction studies on penned white-tailed deer. J. Wildl. Manage. 29:74-79. 1969. Reproductive patterns of white-tailed deer related to nutritional plane. J. Wildl. Manage. 33:881-887. , L. D. FAY, AND U. V. MOSTOSKY. 1962. Use of x-ray in determining pregnancy in deer. J. Wildl. Manage. 26:409-411. ZWANK, P. J. 1981. Effects of field laparotomy on survival and reproduction of mule deer. J. Wildl. Manage. 45:972-975.
Wavelength weightings in machine learning for ovine joint tissue differentiation using diffuse reflectance spectroscopy (DRS).

Objective: To investigate the DRS of ovine joint tissue to determine the optimal optical wavelengths for tissue differentiation and relate these wavelengths to the biomolecular composition of tissues. In this study, we combine machine learning with DRS for tissue classification and then look further at the weighting matrix of the classifier to further understand the key differentiating features. Methods: Supervised machine learning was used to analyse DRS data. After normalising the data, dimension reduction was achieved through multiclass Fisher's linear discriminant analysis (Multiclass FLDA) and classified with linear discriminant analysis (LDA). The classifier was first run with all the tissue types and the wavelength range 190 nm - 1081 nm. We analysed the weighting matrix of the classifier and then ran the classifier again, the first time using the ten highest weighted wavelengths and the second using only the single highest. Our method was applied to a dataset containing ovine joint tissue including cartilage, cortical and subchondral bone, fat, ligament, meniscus, and muscle. Results: It achieved a classification accuracy of 100% using the wavelength 190 nm - 1081 nm (2048 attributes) with an accuracy of 90% being present for 10 attributes with the exception of those with comparable compositions such as ligament and meniscus. An accuracy greater than 70% was achieved using a single wavelength, with the same exceptions. Conclusion: Multiclass FLDA combined with LDA is a viable technique for tissue identification from DRS data. The majority of differentiating features existed within the wavelength ranges 370-470 and 800-1010 nm. Focusing on key spectral regions means that a spectrometer with a narrower range can potentially be used, with less computational power needed for subsequent analysis.
Laparoscopic rectal dissection preserves erectile function after ileal pouch–anal anastomosis: a two‐centre study

Few studies have been published on erectile function after ileal pouch–anal anastomosis (IPAA) and, unlike in women, male fertility after IPAA has never been assessed. The primary objective was to assess the impact of IPAA on erectile function. The secondary objective was to assess the impact of IPAA on male fertility.
Nomogram to predict risk for early ischemic stroke by non-invasive method

Abstract Stroke is the acute onset of neurological deficits and is associated with high morbidity, mortality, and disease burden. In the present study, we aimed to develop a scientific, nomogram for non-invasive predicting risk for early ischemic stroke, in order to improve stroke prevention efforts among high-risk groups. Data were obtained from a total of 2151 patients with early ischemic stroke from October 2017 to September 2018 and from 1527 healthy controls. Risk factors were examined using logistic regression analyses. Nomogram and receiver operating characteristic (ROC) curves were drawn, cutoff values were established. Significant risk factors for early ischemic stroke included age, sex, blood pressure, history of diabetes, history of genetic, history of coronary heart disease, history of smoking. A nomogram predicting ischemic stroke for all patients had an internally validated concordance index of 0.911. The area under the ROC curve for the logistic regression model was 0.782 (95% confidence interval [CI]: 0.766–0.799, P < .001), with a cutoff value of 2.5. The nomogram developed in this study can be used as a primary non-invasive prevention tool for early ischemic stroke and is expected to provide data support for the revision of current guidelines.
Root Proliferation and Nutrient Limitations in a Nicaraguan Rain Forest

Abstract. Knowledge of plant nutrient limitations within natural and agricultural ecosystems is important for a full understanding of the ecology of plant populations and communities. While broad generalizations have been made for wet tropical forests there are few studies that directly address the question of nutrient limitations. The lack of research, in part, is due to the time and expense of traditional long-term fertilization experiments that examine ecosystem productivity under different nutrient regimes. To identify nutrient limitations within a lowland tropical rainforest we utilized an alternative method, the root ingrowth-core technique, which uses nutrient enriched substrates implanted into the forest soil. Over time root growth into the enriched substrates is greatest in those containing limiting nutrients. In addition, we analyzed intact soil cores from the forest floor for nutrients and root length density to see if natural nutrient variations were sufficient to elicit changes in root proliferation. We found that root ingrowth cores as well as soil cores showed greater root length in cores richer in phosphorus and nitrogen. Comparisons between root ingrowth core treatments revealed no differences in root width. However, overall root width was greater in the ingrowth cores than in the forest soil. While most authors suggest that phosphorus and nutrient cations (e.g., K, Mg, and Ca) tend to be limiting in lowland tropical forests, our study suggests that both phosphorus and nitrogen but not potassium are in limited supply within the forest studied.
The genetic characterization of Northeastern Quercus associated Xylella fastidiosa populations

OF THE DISSERTATION.ii ACKNOWLEDGEMENTS.iv TABLE OF CONTENTS.v LIST OF TABLES.viii LIST OF FIGURES.ix CHAPTER 1. Literature Review.1 Historical Overview Leading to the Advent of Molecular Techniques.1 Early Molecular Techniques and Population Profiling to the first X. fastidiosa genome release.3 Early Genetic Characterizations, Multilocus Sequencing Analysis (MLSA), and Continued Population and Speciation Studies.6 Expansion of Isolate Sequencing, Large Scale Comparative Genomics, and the Extension into Targeted Locus-Based Research.9 Prophage Elements in X. fastidiosa Genomes and Significance in Bacterial Population Distribution and Structure.11 References.14 CHAPTER 2. “The genetic composition of oak associated X. fastidiosa populations in the Northeastern and Mid-Atlantic United States”. 23 Abstract.23 v
Clinical utility of Epstein‐Barr virus DNA and other liquid biopsy markers in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor ubiquitously associated with the Epstein‐Barr virus (EBV), which is highly prevalent in South China, Southeast Asia, and North Africa. Despite being a highly radio‐sensitive and treatable cancer, a majority of NPC patients are diagnosed in their advanced stage, and locoregional and distant relapses following definitive treatment contribute largely to cancer‐specific mortality among these patients. Given that EBV‐driven NPC is the predominant variant seen in endemic regions, various EBV detection methods have been developed and are utilized in screening, prognostication, and post‐treatment surveillance of NPC patients. While the Immunoglobulin A (IgA) serology assay is the most extensively studied EBV detection method, the detection of plasma EBV DNA released during replication or cellular apoptosis has shown superior outcomes in endemic population screening, prognostication, and detection of distant relapse. Furthermore, there is emerging evidence on the use of circulating tumor cells, microRNAs, DNA hypermethylation, and combination assays in various clinical scenarios. Herein, this paper provides a comprehensive overview of the relevant studies using various EBV detection techniques in the management of NPC. Specifically, the recent advances, clinical evidence, and challenges associated with the clinical application of EBV liquid biopsies in population screening, prognostication, and surveillance of NPC are presented.
Economics of Weed Management in Glufosinate-Resistant Corn (Zea mays L.)1

Abstract: Field experiments were conducted in 1997 and 1998 near Columbia and Novelty, MO, and at Urbana, IL, to evaluate corn injury, weed control, corn yield, and estimated economic returns with weed management programs in glufosinate-resistant corn. Herbicide programs included acetochlor preemergence (PRE) followed by glufosinate alone or with atrazine postemergence (POST) and total POST programs consisting of single and sequential applications of glufosinate alone or tank mixed with acetochlor, atrazine, or acetochlor plus atrazine. Metolachlor PRE followed by dicamba plus atrazine early POST (EPOST) and metolachlor plus atrazine PRE were included for comparison. In the total POST treatments, mid-POST applications controlled shattercane and common cocklebur better than EPOST applications. However, yield reductions as high as 23% occurred because of early-season weed interference, although weeds were controlled later in the season. Applying atrazine with glufosinate generally increased control of giant foxtail, common cocklebur, morningglory species, and common waterhemp compared to glufosinate alone, but did not increase control of common lambsquarters, velvetleaf, or Pennsylvania smartweed. Corn yield was positively correlated with weed control (r = 0.88) and more strongly dependent on grass (r = 0.82) than broadleaf (r = 0.70) weed control. Net incomes were positively correlated to corn yield (r = 0.73). Four of the top six net income-producing treatments included two herbicide applications. Three of the treatments were PRE followed by POST programs, and the fourth was a sequential POST treatment of glufosinate. Nomenclature: Acetochlor; atrazine; dicamba; glufosinate; metolachlor; common cocklebur, Xanthium strumarium L. #3 XANST; common lambsquarters, Chenopodium album L. # CHEAL; common waterhemp, Amaranthus rudis Sauer # AMATA; giant foxtail, Setaria faberi (L.) Herrm. # SETFA; morningglory, Ipomoea spp. ; Pennsylvania smartweed, Polygonum pensylvanicum L. # POLPY; shattercane, Sorghum bicolor (L.) Moench. # SORVU; velvetleaf, Abutilon theophrasti (L.) Medikus # ABUTH; corn, Zea mays L. # ZEAMX ‘Pioneer 34A55’. Additional index words: Corn yield, economic returns, glufosinate-resistant crop, AMATA, ABUTH, CHEAL, POLPY, SETFA, SORVU, XANST, ZEAMX. Abbreviations: ALS, acetolactate synthase; CV, coefficient of variation; EPOST, early postemergence; MPOST, mid-postemergence; POST, postemergence; PRE, preemergence; WAT, weeks after treatment.
Geosynchronous Satellite GF-4 Observations of Chlorophyll-a Distribution Details in the Bohai Sea, China

We analyzed the distribution of chlorophyll-a (Chla) in the Bohai Sea area based on data from the geosynchronous orbit optical satellite Gaofen-4 (GF-4), which was launched in 2015, carrying a panchromatic multispectral sensor (PMS). This is the first time the geosynchronous orbit optical satellite GF-4 remote-sensing data has been used in China to detect the Chla change details in the Bohai Sea. A new GF-4 retrieved model was established based on the relationship between in situ Chla value and the reflectance combination of 2 and 4 bands, with the R2 of 0.9685 and the total average relative error of 37.42%. Twenty PMS images obtained from 2017 to 2019 were applied to analyze Chla in Bohai sea. The results show that: (1) the new built Chla inversion model PMS-1 for the GF-4 PMS sensor can extract Chla distribution details in the Bohai Sea well. The high Chla content in the Bohai Sea is mainly located in coastal areas, such as the top of Laizhou Bay, Bohai Bay and Liaodong Bay, with the value being around 13 µg/L. The concentration of Chla in the Bohai Strait and northern Yellow Sea is relatively low with the value being around 5 µg/L. (2). Taking full advantage of the continuous observation of geostationary orbit satellite, GF-4 with a high-resolution sensor PMS of 50 m can effectively detect short-term change (changes within 10 min) in Chla concentration. The changes mainly appear at the southwest and northeast costal area as well as in the center of Bohai Sea with the change value of around 3 µg/L. (3) The change of Chla concentration in the Bohai sea is related to the environmental factors such as seawater temperature, salinity, illumination and nutrient salts, as well as the dynamic factors such as wind, flow field and tidal current.
Impact of improved wheat technology adoption on productivity and income in Ethiopia

Wheat ( Triticum aestivum L.) is one of the most important cereal crops cultivated in wide range of agro-ecologies in Eastern Africa. However, wheat productivity has remained low. This study was carried out in Ethiopia Aris Zone to determine the level and impact of adoption of improved wheat varieties on wheat productivity and farm income level of wheat producers in the country. The study employed the propensity score matching method to carry out the impact study. It was found out that the rate of adoption of improved wheat varieties in 2013 was 56%. Probit model showed that sex of household headship and livestock ownership enhanced adoption of improved varieties, while the educational level of the household head negatively affected in enhancing the adoption of improved wheat varieties. According to the result of the propensity score matching method, improved wheat variety adoption on average increased wheat productivity of adopters by about 1 to 1.1 t ha-1 than the nonadopters. Similarly, the result of the propensity score matching estimates showed that the average income of adopters was 35 to 50% greater than the non-adopters.The results provide empirical evidence that agricultural technology adoption can contribute to improving productivity and raising income of farm households. Key Words : Adoption, Probit and Propensity Score Matching, Triticum aestivum
Fast Lasso method for Large-scale and Ultrahigh-dimensional Cox Model with applications to UK Biobank

We develop a scalable and highly efficient algorithm to fit a Cox proportional hazard model by maximizing the L1-regularized (Lasso) partial likelihood function, based on the Batch Screening Iterative Lasso (BASIL) method developed in (Qian et al. 2019). The output of our algorithm is the full Lasso path, the parameter estimates at all predefined regularization parameters, as well as their validation accuracy measured using the concordance index (C-index) or the validation deviance. To demonstrate the effectiveness of our algorithm, we analyze a large genotype-survival time dataset across 306 disease outcomes from the UK Biobank (Sudlow et al. 2015). Our approach, which we refer to as snpnet-Cox, is implemented in a publicly available package.
Efficacy of Metformin and Chemotherapeutic Agents on the Inhibition of Colony Formation and Shh/Gli1 Pathway: Metformin/Docetaxel Versus Metformin/5-Fluorouracil

Abstract Background Gastric cancer is a common gastrointestinal cancer characterized by poor prognosis and chemoresistance. Docetaxel and 5-fluorouracil (5-FU) are frequently used for the treatment of gastric cancer. Despite their potent anti-cancer effects, chemoresistance occurs in metastatic gastric cancer. Metformin, a popular anti-diabetic drug, has been proven to have potent anticancer effects on gastrointestinal cancers. Here, we aim to improve this chemotherapy agents’ efficacy by pretreatment with metformin. Methods The AGS gastric cancer cell line were pretreated with three different sub-toxic concentration of metformin and then treated with various concentrations of 5-FU and docetaxel. The anticancer effects of the combination of metformin with the chemotherapy agents were determined using clonogenic assay and DAPi staining. We used real-time PCR to evaluate Gli1, Gli2, and TWIST1 mRNA expression levels in the gastric cancer cells. Also, the expression of the Shh protein was assessed using immunocytochemistry. Results Here, we found that metformin sensitized the gastric cancer cells to chemotherapy. The combination treatments were more effective in reducing the number of cancer colonies compared to 5-FU or docetaxel alone. The combination of metformin with 5-FU or docetaxel significantly reduced the number of cells expressing the Shh protein compared to the 5-FU alone or docetaxel alone. Interestingly, we found that the combination of metformin with docetaxel significantly down-regulated the mRNA levels of Gli1, Gli2, and TWIST1 in the AGS gastric cancer cell line compared to docetaxel alone. Conclusion Overall, our data strongly support an important role for metformin as an enhancer of the efficacy of chemotherapeutic agents against gastric cancer.