Miracle-dz/UniFAR-FTUs huggingface dataset:
Clustering-Correcting Codes

A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the form of unordered sequences, also called strands, and every strand is synthesized thousands to millions of times, where some of these copies are read back during sequencing. Due to the unordered structure of the strands, an important task in the decoding process is to place them in their correct order. This is usually accomplished by allocating a part of the strand for an index. However, in the presence of errors in the index field, important information on the order of the strands may be lost.Clustering-correcting codes ensure that if the distance between the index fields of two strands is small, then there will be a large distance between their data fields. It is shown how this property enables to place the strands together in their correct clusters even in the presence of errors. We present lower and upper bounds on the size of clustering-correcting codes and an explicit construction of these codes which uses only a single bit of redundancy.
Prevalences of Pospiviroid Contamination in Large Seed Lots of Tomato and Capsicum, and Related Seed Testing Considerations

Analyses of pospiviroids in commercial seed lots of tomato and capsicum, determined by testing of 12,000 to 40,000 seeds per lot, have enabled the development of empirically-derived distribution curves for the observed prevalences of viroids in those commodities. Those distribution curves can be considered in conjunction with statistically-based estimates of detection that would be achieved using other sample sizes. Statistical calculations using binomial distributions show that sample sizes of 3000 and 9400 seeds allow detection of viroid prevalences as low as 0.1% and 0.032%, respectively, with 95% confidence. Applying those calculations to observed viroid prevalences in contaminated tomato seed lots, it is estimated that the use of sample sizes of 3000 and 9400 seeds would detect 15% and 42%, respectively, of the contaminated seed lots identified using the larger sample sizes of approximately 20,000 seeds reported in this study. It is concluded that the higher costs associated with testing of larger sample sizes represent a worthwhile investment in agricultural biosecurity.
A Room-Temperature Autonomically-Healing PMMA Bone Cement: Influence of Composition on Fatigue Crack Propagation Rate

Purpose: To test two hypotheses. First, autonomic healing is achievable in a commercially available poly (methyl methacrylate) bone cement brand that is widely used to anchor total joint replacements. Secondly, in this self-healing cement, the fatigue crack propagation (FCP) rate is critically dependent on the relative amount of the mass of the healing agent (endoisomer of dicyclopentadiene (DCPD) embedded in poly (urea-formaldehyde) (PUF) microcapsules (diameter = 226 ± 51 μm)) (MDM) to that of the catalyst (a first-generation Grubbs’ catalyst) (MGC). (Note that, in this work, the term, “autonomic healing” or “self healing”, refers to the ability of the material, after having been damaged during service, due to formation of cracks, for example, to restore its initial mechanical performance without the need for any external intervention). Methods: The strategy that was developed by White et al. for room-temperature autonomic healing of a neat polymeric material was used. The DCPD-filled PUF microcapsules and the catalyst were blended with the cement’s powder in a mortar bowl using a polymeric spatula, and the blended powder mixture and the cement’s liquid monomer were mixed under a partial vacuum. FCP tests were performed on specimens of seven study groups: the control cement (CMWTM1), four sets having different values of MDM/MGC, one set in which only the DCPD-filled microcapsules were blended with the CMW TM1 powder, and one set in which only the Grubbs’ catalyst was blended with the CMWTM1 powder. Results: An index of the self-healing achieved, as computed using the estimated FCP rates, was within the range reported in the literature for autonomically-healing neat polymeric materials. Furthermore, the variation of the estimated FCP rate with MDM/MGC suggests that changes in this rate is critically dependent on change of MDM/MGC. Conclusion: The results supported both of the study hypotheses (Journal of Applied Biomaterials & Biomechanics 2009; 7: 90-6).
Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate

Abstract The persistence of an invasive species is influenced by its reproductive ecology, and a successful control program must operate on this premise. However, the reproductive ecology of invasive species may be enigmatic due to factors that also limit their management, such as cryptic coloration and behavior. We explored the mating and reproductive ecology of the invasive Brown Treesnake (BTS: Boiga irregularis) by reconstructing a multigenerational genomic pedigree based on 654 single nucleotide polymorphisms for a geographically closed population established in 2004 on Guam (N = 426). The pedigree allowed annual estimates of individual mating and reproductive success to be inferred for snakes in the study population over a 14‐year period. We then employed generalized linear mixed models to gauge how well phenotypic and genomic data could predict sex‐specific annual mating and reproductive success. Average snout–vent length (SVL), average body condition index (BCI), and trappability were significantly related to annual mating success for males, with average SVL also related to annual mating success for females. Male and female annual reproductive success was positively affected by SVL, BCI, and trappability. Surprisingly, the degree to which individuals were inbred had no effect on annual mating or reproductive success. When juxtaposed with current control methods, these results indicate that baited traps, a common interdiction tool, may target fecund BTS in some regards but not others. Our study emphasizes the importance of reproductive ecology as a focus for improving BTS control and promotes genomic pedigree reconstruction for such an endeavor in this invasive species and others.
A Clustering-Based Combinatorial Approach to Unsupervised Matching of Product Titles

The constant growth of the e-commerce industry has rendered the problem of product retrieval particularly important. As more enterprises move their activities on the Web, the volume and the diversity of the product-related information increase quickly. These factors make it difficult for the users to identify and compare the features of their desired products. Recent studies proved that the standard similarity metrics cannot effectively identify identical products, since similar titles often refer to different products and vice-versa. Other studies employed external data sources (search engines) to enrich the titles; these solutions are rather impractical mainly because the external data fetching is slow. In this paper we introduce UPM, an unsupervised algorithm for matching products by their titles. UPM is independent of any external sources, since it analyzes the titles and extracts combinations of words out of them. These combinations are evaluated according to several criteria, and the most appropriate of them constitutes the cluster where a product is classified into. UPM is also parameter-free, it avoids product pairwise comparisons, and includes a post-processing verification stage which corrects the erroneous matches. The experimental evaluation of UPM demonstrated its superiority against the state-of-the-art approaches in terms of both efficiency and effectiveness.
Influence of Nitrogen Limitation on Lipid Accumulation and EPA and DHA Content in Four Marine Microalgae for Possible Use in Aquafeed

Microalgae are regarded as a promising alternative that can replace fishmeal and fish oil in aquaculture. Under N-limitation, many microalgae species change their carbon storage patterns in favor of neutral lipids (NLs) mainly in the form of triacylglycerol (TAG), but fatty acids in polar lipids (PL) are nutritionally more available for fish than those esterified into NLs. In the present study, the effect of N-limitation on the lipid content and fatty acid profiles in different lipid class of Phaeodactylum tricornutum, Isochrysis aff. galbana clone T-Iso, Rhodomonas baltica and Nannochloropsis oceanica were investigated. The microalgae cells were cultivated by two different methods, batch and semi-continuous culture, to create strong and moderate N-limitation, and this in turn will significantly affect the biomass and lipid productivity. All four species accumulated lipids mainly in the form of TAG in response to strong nitrogen limitation. N. oceanica, however accumulated 51% of the dry weight as lipid in moderate nitrogen limitation and up to 87% of the fatty acid was in TAG. Isochrysis aff. galbana clone T-Iso was the only species where the fraction of polyunsaturated fatty acid (PUFA), especially the fraction of docosahexaenoic acid (DHA) increased with increasing nitrogen limitation. Total lipid productivity showed no increase in batch culture although stronger nitrogen limitation led to lipid accumulation. P. tricornutum had the highest eicosapentaenoic acid (EPA) content, while N. oceanica showed the highest EPA productivity due to the high content of lipid. The highest DHA productivity was found in Isochrysis aff. galbana clone T-Iso from moderate N-limitation mainly due to the high biomass productivity. Based on the results from the current study, N. oceanica and T-Iso are two promising microalgae strains as long-term sustainable source of n-3 long chain -PUFAs under moderate N-limitation. As shown in the present study, increased lipid content in microalgal cells due to strong N-limitation induction may not increase the lipid productivity because biomass production usually is reduced. Therefore, a combination of approaches such as metabolic engineering, conditioning and selection may be needed to further increase the n-3 LC-PUFA productivity without substantial loss of biomass.
Ultrasound-Assisted Lumbar Interlaminar Epidural Dye Injection and Evaluation of Its Distribution by Anatomical Dissection

Background: Epidural steroid injections are frequently used to treat lumbar radicular pain. However, the spread of a solute in the epidural space needs further elucidation. We aimed at assessing the distribution of green dye in the epidural space after lumbar epidural injection on cadavers. Methods: We performed ultrasound-guided injections of green dye between lumbar vertebrae 4 and 5 in 24 cadavers. The cadavers were randomly divided into group A and B according to the volume of injected dye; 3 ml in group A (n = 13) and 6 ml in group B (n = 11). Accuracy of the needle insertion and patterns and distributions of the spread were compared between the groups. After local dissection, we examined the spread of dye in dorsal and ventral epidural spaces and presented the distribution as whole numbers and quartiles of intervertebral segments. Mann-Whitney U Test was used to compare distribution of dye spread between groups A and B. Wilcoxon Signed-Rank Test was used to compare the spread of dye in cranial and caudal direction within the group. We considered P < 0.05 as significant. Results: Data were obtained from all 24 cadavers. Median levels of dorsal cranial dye distribution in groups A and B were 2 and 4 (P = 0.02), respectively. In the dorsal caudal−2 and 2, respectively (P = 0.04). In the ventral epidural space cranial dye spread medians were−0 and 2 in groups, respectively (P = 0.04). Ventral caudal spread was 0 and 1, respectively (P = 0.03). We found a significant difference between cranial and caudal dye distribution in group B (P < 0.05). In group A the dye spread was bilateral. In group B cranial and caudal dye spread was observed. Conclusions: Ventral dye flow was observed in 50% of injections. Bilateral spread of dye occurred in 63%, and more often in group A. Cranial spread was slightly higher than caudal spread in group A despite a smaller injected volume, and significantly higher in group B following a larger volume.
Mutating for Good: DNA Damage Responses During Somatic Hypermutation

Somatic hypermutation (SHM) of immunoglobulin (Ig) genes plays a key role in antibody mediated immunity. SHM in B cells provides the molecular basis for affinity maturation of antibodies. In this way SHM is key in optimizing antibody dependent immune responses. SHM is initiated by targeting the Activation-Induced Cytidine Deaminase (AID) to rearranged V(D)J and switch regions of Ig genes. The mutation rate of this programmed mutagenesis is ~10−3 base pairs per generation, a million-fold higher than the non-AID targeted genome of B cells. AID is a processive enzyme that binds single-stranded DNA and deaminates cytosines in DNA. Cytosine deamination generates highly mutagenic deoxy-uracil (U) in the DNA of both strands of the Ig loci. Mutagenic processing of the U by the DNA damage response generates the entire spectrum of base substitutions characterizing SHM at and around the initial U lesion. Starting from the U as a primary lesion, currently five mutagenic DNA damage response pathways have been identified in generating a well-defined SHM spectrum of C/G transitions, C/G transversions, and A/T mutations around this initial lesion. These pathways include (1) replication opposite template U generates transitions at C/G, (2) UNG2-dependent translesion synthesis (TLS) generates transversions at C/G, (3) a hybrid pathway comprising non-canonical mismatch repair (ncMMR) and UNG2-dependent TLS generates transversions at C/G, (4) ncMMR generates mutations at A/T, and (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)-dependent mutations at A/T. Furthermore, specific strand-biases of SHM spectra arise as a consequence of a biased AID targeting, ncMMR, and anti-mutagenic repriming. Here, we review mammalian SHM with special focus on the mutagenic DNA damage response pathways involved in processing AID induced Us, the origin of characteristic strand biases, and relevance of the cell cycle.
Comparative Description of the Expression Profile of Interferon-Stimulated Genes in Multiple Cell Lineages Targeted by HIV-1 Infection

Immediately after viral infections, innate immune sensors recognize viruses and lead to the production of type I interferon (IFN-I). IFN-I upregulates various genes, referred to as IFN-stimulated genes (ISGs), and some ISGs inhibit viral replication. HIV-1, the causative agent of AIDS, mainly infects CD4+ T cells and macrophages and triggers the IFN-I-mediated signaling cascade. Certain ISGs are subsequently upregulated by IFN-I stimulus and potently suppress HIV-1 replication. HIV-1 cell biology has shed light on the molecular understanding of the IFN-I production triggered by HIV-1 infection and the antiviral roles of ISGs. However, the differences in the gene expression patterns following IFN-I stimulus among HIV-1 target cell types are poorly understood. In this study, we hypothesize that the expression profiles of ISGs are different among HIV-1 target cells and address this question by utilizing public transcriptome datasets and bioinformatic techniques. We focus on three cell types intrinsically targeted by HIV-1, including CD4+ T cells, monocytes, and macrophages, and comprehensively compare the expression patterns of ISGs among these cell types. Furthermore, we use the datasets of the differentially expressed genes by HIV-1 infection and the evolutionarily conserved ISGs in mammals and perform comparative transcriptome analyses. We defined 104 ‘common ISGs’ that were upregulated by IFN-I stimulus in CD4+ T cells, monocytes, and macrophages. The ISG expression patterns were different among these three cell types, and intriguingly, both the numbers and the magnitudes of upregulated ISGs by IFN-I stimulus were greatest in macrophages. We also found that the upregulated genes by HIV-1 infection included most ‘common ISGs. ’ Moreover, we determined that the ‘common ISGs,’ particularly those with antiviral activity, were evolutionarily conserved in mammals. To our knowledge, this study is the first investigation to comprehensively describe (i) the different expression patterns of ISGs among HIV-1 target cells, (ii) the overlap in the genes modulated by IFN-I stimulus and HIV-1 infection and (iii) the evolutionary conservation in mammals of the antiviral ISGs that are expressed in HIV-1 target cells. Our results will be useful for deeply understanding the relationship of the effect of IFN-I and the modulated gene expression by HIV-1 infection.
Activity and Impact on Resistance Development of Two Antivirulence Fluoropyrimidine Drugs in Pseudomonas aeruginosa

The rise in antibiotic resistance among bacterial pathogens has prompted the exploitation of alternative antibacterial strategies, such as antivirulence therapy. By inhibiting virulence traits, antivirulence drugs are expected to lessen pathogenicity without affecting bacterial growth, therefore avoiding the spread of resistance. However, some studies argued against this assumption, and the lack of antivirulence drugs in clinical use hampers the empirical assessment of this concept. Here we compared the mode of action and range of activity of two drugs which have been proposed for repurposing as quorum sensing and pyoverdine inhibitors in the human pathogen Pseudomonas aeruginosa: the anticancer drug 5-fluorouracil (5-FU) and the antimycotic drug 5-fluorocytosine (5-FC), respectively. The effect on bacterial growth, emergence and spread of resistance, and activity against clinical isolates were assessed. Our results confirm that 5-FU has growth inhibitory activity on reference strains and can rapidly select for spontaneous resistant mutants with loss-of-function mutations in the upp gene, responsible for uracil conversion into UMP. These mutants were also insensitive to the anti-pyoverdine effect of 5-FC. Conversely, 5-FC did not cause relevant growth inhibition, likely because of poor enzymatic conversion into 5-FU by cytosine deaminase. However, coculturing experiments showed that 5-FU resistant mutants can outcompete sensitive cells in mixed populations, in the presence of not only 5-FU but also 5-FC. Moreover, we observed that serial passages of wild-type cells in 5-FC-containing medium leads to the appearance and spread of 5-FC insensitive sub-populations of 5-FU resistant cells. The different effect on growth of 5-FU and 5-FC was overall conserved in a large collection of cystic fibrosis (CF) isolates, corresponding to different infection stages and antibiotic resistance profiles, although high variability was observed among strains. Notably, this analysis also revealed a significant number of pyoverdine-deficient isolates, whose proportion apparently increases over the course of the CF infection. This study demonstrates that the efficacy of an antivirulence drug with no apparent effect on growth can be significantly influenced by the emergence of insensitive mutants, and highlights the importance of the assessment of resistance-associated fitness cost and activity on clinical isolates for the development of “resistance-proof” antivirulence drugs.
Current perspectives on recurrent pituitary adenoma: The role and timing of surgery vs adjuvant treatment

The clinical course of pituitary adenoma can be highly variable. Aggressive pituitary tumours may require multimodal therapy with multiple operations. Even standard pituitary adenomas exhibit relatively high long‐term recurrence rates and delayed intervention is often required. The indications for revision surgery in the endoscopic era are expanding for both functioning and nonfunctioning tumours, including access to the cavernous sinus and intracranial compartments. Although revision surgery can be challenging, it has been demonstrated to be both safe and effective. The question of the use of early radiotherapy in pituitary adenoma remains controversial. Our increasing understanding of pituitary tumour biology facilitates individualized treatment and surveillance protocols, with early intervention in high‐risk adenoma subtypes. In this review, we discuss the treatment options for recurring pituitary tumours and focus on the role of revision surgery.
Super-Low Dose Lipopolysaccharide Dysregulates Neutrophil Migratory Decision-Making

Neutrophils are the first responders to infection and play a pivotal role in many inflammatory diseases, including sepsis. Recent studies have shown that lipopolysaccharide (LPS), a classical pattern recognition molecule, dynamically programs innate immune responses. In this study, we show that pre-treatment with super-low levels of LPS [1 ng/mL] significantly dysregulate neutrophil migratory phenotypes, including spontaneous migration and altering neutrophil decision-making. To quantify neutrophil migratory decision-making with single-cell resolution, we developed a novel microfluidic competitive chemotaxis-chip (μC3) that exposes cells in a central channel to competing chemoattractant gradients. In this reductionist approach, we use two chemoattractants: a pro-resolution (N-Formyl-Met-Leu-Phe, fMLP) and pro-inflammatory (Leukotriene B4, LTB4) chemoattractant to model how a neutrophil makes a decision to move toward an end target chemoattractant (e.g., bacterial infection) vs. an intermediary chemoattractant (e.g., inflammatory signal). We demonstrate that naïve neutrophils migrate toward the primary end target signal in higher percentages than toward the secondary intermediary signal. As expected, we found that training with high dose LPS [100 ng/mL] influences a higher percentage of neutrophils to migrate toward the end target signal, while reducing the percentage of neutrophils that migrate toward the intermediary signal. Surprisingly, super-low dose LPS [1 ng/mL] significantly changes the ratios of migrating cells and an increased percentage of cells migrate toward the intermediary signal. Significantly, there was also an increase in the numbers of spontaneously migrating neutrophils after treatment with super-low dose LPS. These results shed light onto the directional migratory decision-making of neutrophils exposed to inflammatory training signals. Understanding these mechanisms may lead to the development of pro-resolution therapies that correct the neutrophil compass and reduce off-target organ damage.
A Novel Microbiological Method in Microtiter Plates for Screening Seven Kinds of Widely Used Antibiotics Residues in Milk, Chicken Egg and Honey

A broad-spectrum microbiological inhibition method has been developed for rapidly screening different kinds of antibiotics such as β-lactam, aminoglycosides, tetracyclines, sulfonamides, macrolides, lincosamides and quinolones in milk, chicken egg and honey by using an easy sample preparation. The microbiological system in microtiter plates consists of an agar medium, a mixture of nutrients, test bacteria (Geobacillus stearothermophilus var C953), bromocresol purple, and other supplements such as trimethoprim, chloramphenicol, streptomycin and enrofloxacin which helps to improve the detection capability of the microbiological system toward the chosen antibiotics. It was observed that the limit of detection of the kit used in present study for all kinds of antibiotics in milk were lower than or close to maximum residue limits determined by EU or CODEX. For chicken egg and honey, the detection capability of the kit was similar to that determined in milk. Moreover, it was revealed that the kit in present study was more sensitive to aminoglycosides, macrolides and quinolones in various matrixes than internationally available commercial kits. The false-positive and false-negative rates for both were 0%. The coefficient of variations among various factors was all less than 4%. Additionally, the quality guarantee period of the kit was more than 6 months at 4°C. A good correlation between the kit results and the LC–MS/MS results for milk was also observed, which revealed that the kit was reliable to screen antibiotics residues in incurred samples.