Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning, sequence analysis, and expression of CIDR1α-PfEMP1 from Indonesian Plasmodium falciparum isolate

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is an antigenic protein which is expressed in the erythrocytic phase of P. falciparum life cycle and plays an essential role in severe malaria pathogenesis. It is encoded by the var gene family and consists of cysteine-rich interdomain region (CIDR) and Duffy-binding-like (DBL) domains. This research aimed to clone, analyze, and express the CIDR1α-PfEMP1 from Indonesian P. falciparum isolate. The specific CIDR1α domain was amplified from malaria patients. The amplicon was ligated into pET-30a and transformed into Escherichia coli BL21(DE3). Sequencing result of plasmid clones confirmed 100% homology with the sequence of the CIDR1α domain. BLAST analysis showed that the sequence had high similarity to Plasmodium sp. gorilla clade G1 from Africa and P. falciparum isolate from Tanzania, East Africa. Translation using ExPASy Translate Tool resulted in a truncated protein consisting of 99 amino acids. Western blot analysis using anti-His-6-tag antibody showed that the recombinant protein was a 17.5 kDa fusion protein and clearly expressed as a soluble protein when induced with 0.1 mM isopropylthio-β-galactoside (IPTG) for ≥8 hours at room temperature. As much as 45.4% of amino acids showed 100% homology with other human-infecting P. falciparum isolates. The sequence was predicted to have B-cell epitope based on immune epitope database. In conclusion, Indonesian CIDR1α-PfEMP1 isolate had high similarity to primate and humaninfecting Plasmodium spp. isolates. The recombinant protein was expressed as a fusion protein. Its structure prediction showed that the sequences have B-cell epitope, implicating its potency in inducing antibodies. Further studies should be established to develop its potency as a vaccine candidate.
Teaching Programming to Students in other Fields

It is a fact that programming is difficult to learn. On the other hand, programming skills are essential for each program in the field of computing and must be covered in the curriculum, regardless of the profile. Our experience in the last 3-4 years shows a noticeable downward trend in students’ results in computer science and similar programs. In this article, we comment on the reasons that have led to such a decline and we are looking for solutions by experimenting with motivated students from other areas of knowledge and comparing their progress in mastering basic concepts and mechanisms of programming with that of computer specialists.
Guaifenesin as a treatment for primary dysmenorrhea.

BACKGROUND Dysmenorrhea is highly prevalent and causes much work loss and discomfort. A treatment with a new mechanism of action could benefit women of menstruating age. A study was undertaken to assess the efficacy of guaifenesin as a treatment for primary dysmenorrhea because of its effects of cervical dilation and cervical mucous thinning. METHODS Thirty-four subjects with primary dysmenorrhea were enrolled in a double-blind, placebo-controlled study. Three treatment surveys measured 10 symptoms (lower abdominal pain, general abdominal pain, back pain, headache, nausea, diarrhea, constipation, menstrual flow, weakness, and activities of daily living) on a 100-mm visual analog scale. Nonstudy analgesic use was also measured. RESULTS Twenty-five subjects returned the first treatment survey, and 17 returned all 3 surveys. Results were nonsignificant, but guaifenesin trended toward being better than placebo for dysmenorrhea pain and associated constitutional symptoms and caused no worsening of symptoms. Lower abdominal mean pain scores from the first survey decreased 38 mm for guaifenesin versus 7 mm for placebo. By the third survey, only 2 of 8 guaifenesin participants took nonstudy analgesics compared with all 9 placebo subjects. CONCLUSIONS Guaifenesin may be useful in the treatment of primary dysmenorrhea. A larger study is needed to validate these initial findings.
Effective doses in children: association with common complex imaging techniques used during interventional radiology procedures.

OBJECTIVE The purpose of this study was to determine the range of effective doses associated with imaging techniques used during interventional radiology procedures on children. MATERIALS AND METHODS A pediatric phantom set (1, 5, and 10 years) coupled with high-sensitivity metal oxide semiconductor field effect transistor (MOSFET) dosimeters was used to calculate effective doses. Twenty MOSFETs were inserted into each phantom at radiosensitive organ locations. The phantoms were exposed to mock head, chest, and abdominal interventional radiology procedures performed with different geometries and magnifications. Fluoroscopy, digital subtraction angiography (DSA), and spin angiography were simulated on each phantom. Road mapping was conducted only on the 5-year-old phantom. International Commission on Radiological Protection publication 103 tissue weights were applied to the organ doses recorded with the MOSFETs to determine effective dose. For easy application to clinical cases, doses were normalized per minute of fluoroscopy and per 10 frames of DSA or spin angiography. RESULTS Effective doses from DSA, angiography, and fluoroscopy were higher for younger ages because of magnification use and were largest for abdominal procedures. DSA of the head, chest, and abdomen (normalized per 10 frames) imparted doses 2-3 times as high as corresponding doses per minute of fluoroscopy while all other factors remained unchanged (age, projection, collimation, magnification). Three to five frames of DSA imparted an effective dose equal to doses from 1 minute of fluoroscopy. Doses from spin angiography were almost one-half the doses received from an equivalent number of frames of DSA. CONCLUSION Patient effective doses during interventional procedures vary substantially depending on procedure type but tend to be higher because of magnification use in younger children and higher in the abdomen.
The use of a ribosomal RNA targeted oligonucleotide probe for fluorescent labelling of viable Cryptosporidiumparvum oocysts

A fluorescence in situ hybridization (FISH) technique has been developed for the fluorescent labelling of Cryptosporidium parvum oocysts in water samples. The FISH technique employs a fluorescently labelled oligonucleotide probe (Cry1 probe) targeting a specific sequence in the 18S ribosomal RNA (rRNA) of C. parvum. Hybridization with the Cry1 probe resulted in fluorescence of sporozoites within oocysts that were capable of excystation, while oocysts that were dead prior to fixation did not fluoresce. Correlation of the FISH method with viability as measured by in vitro excystation was statistically highly significant, with a calculated correlation coefficient of 0·998. Examination of sequence data for Cryptosporidium spp. other than C. parvum suggests that the Cry1 probe is C. parvum‐specific. In addition, 19 isolates of C.parvum were tested, and all fluoresced after hybridization with the Cry1 probe. Conversely, isolates of C.baileyi and C. muris were tested and found not to fluoresce after hybridization with the Cry1 probe. The fluorescence of FISH‐stained oocysts was not bright enough to enable detection of oocysts in environmental water concentrates containing autofluorescent algae and mineral particles. However, in combination with immunofluorescence staining, FISH enabled species‐specific detection and viability determination of C. parvum oocysts in water samples.
Ex vivo photoacoustic imaging of atherosclerotic carotid plaques

Vulnerability assessment of carotid plaques is vital to prevent atherosclerosis-related mortality and disability. Photoacoustic imaging (PAI) in combination with plane-wave ultrasound (PUS) may have the ability to reveal the composition and the anatomical structure of the plaque, which infers its mechanical properties and vulnerability. In this study, we used PAI and PUS imaging to scan endarterectomy samples ex vivo, targeting intraplaque hemorrhage, and compared the results with those obtained in healthy (porcine) carotids and histology. A fully integrated hand-held photoacoustic probe was used, consisting of a pulsed diode laser (tp = 130 ns, Ep = 1 mJ, λ = 808 nm) and a linear array transducer (fc = 7.5 MHz). Three porcine carotid arteries and six carotid plaque samples were obtained from a local slaughterhouse and hospital respectively, and were mounted to the imaging setup. Data of endarterectomy samples revealed that PAI of carotid plaques at 808 nm wavelength is capable of detecting blood clots, which can be extensions of vasculature in the plaque, intra-plaque hemorrhage, or the result of trauma inflicted on the medial vascularization. Due to calcification and the limited optical penetration, imaging depth was mostly limited to the proximal wall of the samples. The porcine carotids revealed no hemorrhaging, which was corroborated by the lack of PAI contrast.
Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.
Understanding the roles of gingival beta-defensins

Abstract Gingival epithelium produces β-defensins, small cationic peptides, as part of its contribution to the innate host defense against the bacterial challenge that is constantly present in the oral cavity. Besides their functions in healthy gingival tissues, β-defensins are involved in the initiation and progression, as well as restriction of periodontal tissue destruction, by acting as antimicrobial, chemotactic, and anti-inflammatory agents. In this article, we review the common knowledge about β-defensins, coming from in vivo and in vitro monolayer studies, and present new aspects, based on the experience on three-dimensional organotypic culture models, to the important role of gingival β-defensins in homeostasis of the periodontium.
The Impact of MiFID on the European Securities Industry: A Simulation of the Internalizer Behavior on the Italian Stock Market º

The European Union’s Markets in Financial Instruments Directive (MiFID), expected to be implemented by October 2007, significantly modifies the regulation of the European securities industry. It will allow, among other things, investment firms to act as systematic internalizers. A systematic internalizer is an investment firm dealing on own account to execute client orders outside a regulated market or a multilateral trading facility (MTF). Specifically, systematic internalizers are required to publish firm quotes (i.e., to make a market) on liquid shares when dealing for retail quantities. This paper uses unique audit trail order data in order to estimate the fraction of order flow internalized, to evaluate the potential profitability of systematic internalization activity, and to investigate the main factors affecting both the fraction of order flow internalized and the magnitude of systematic internalization profitability. We use actually observed order flow data to simulate the systematic internalization activity. Each order submitted to the market has been scrutinized in order to verify the possibility of internalization based on the joint presence of the following two requirements (expressly requested by the Level 1 law text). First, the quantity of the order is not greater than the estimated standard market size. Second, the price limit of the order is compatible with immediate execution by a systematic internalizer in respect of the best execution principle. Our results provide estimates of the fraction of internalized order flow and the internalization gross trading revenues. We find that the fraction of internalized orders is negatively related to the stock's daily turnover. We also decompose the gross trading revenues in positioning revenues and spread revenues. This decomposition allows us to identify the source of the size and variability of gross trading revenues. Spread revenues are statistically different from zero at 1 percent level, whereas positioning revenues are not statistically different from zero at ten percent level. The variability in the gross trading revenues is mainly driven by the large variability in the positioning revenues.
Liberalization of Trade in Services: Toward a Harmonized ASEAN++ FTA

The East Asian countries are seriously discussing the consolidation of ASEAN+1 FTAs to develop so-called ASEAN++ FTA or RCEP. The detailed analysis of services chapters in the existing ASEAN+1 FTAs gives insights to services trade liberalization in this new trade agreement. In order for ASEAN and its FTA partners to gain substantial new commitments that are genuinely "plus" to the existing trade pacts, both WTO GATS and ASEAN+1 FTAs, ASEAN++ countries should aim at an ambitious level of liberalization much higher than the AFAS package 5. Also, the detailed analysis suggests a policy option of narrowing the types of services trade limitations, i.e., focusing on three types of limitations and hence improving transparency. Furthermore, we advocate for the needs of prioritizing production-related services sectors in the negotiation. Beyond ASEAN++ FTA, we briefly explain the critical roles of domestic regulatory reform.
Deletion of Smad2 in Mouse Liver Reveals Novel Functions in Hepatocyte Growth and Differentiation

ABSTRACT Smad family proteins Smad2 and Smad3 are activated by transforming growth factor β (TGF-β)/activin/nodal receptors and mediate transcriptional regulation. Although differential functional roles of Smad2 and Smad3 are apparent in mammalian development, the relative functional roles of Smad2 and Smad3 in postnatal systems remain unclear. We used Cre/loxP-mediated gene targeting for hepatocyte-specific deletion of Smad2 (S2HeKO) in adult mice and generated hepatocyte-selective Smad2/Smad3 double knockouts by intercrossing AlbCre/Smad2f/f (S2HeKO) and Smad3-deficient Smad3ex8/ex8 (S3KO) mice. All strains were viable and had normal adult liver. However, necrogenic CCL4-induced hepatocyte proliferation was significantly increased in S2HeKO compared to Ctrl and S3KO livers, and transplanted S2HeKO hepatocytes repopulated recipient liver at dramatically increased rates compared to Ctrl hepatocytes in vivo. Using primary hepatocytes, we found that TGF-β-induced G1 arrest, apoptosis, and epithelial-to-mesenchymal transition in Ctrl and S2HeKO but not in S3KO hepatocytes. Interestingly, S2HeKO cells spontaneously acquired mesenchymal features characteristic of epithelial-to-mesenchymal transition (EMT). Collectively, these results demonstrate that Smad2 suppresses hepatocyte growth and dedifferentiation independent of TGF-β signaling. Smad2 is not required for TGF-β-stimulated apoptosis, EMT, and growth inhibition in hepatocytes.
Excimer laser phototherapeutic keratectomy in eyes with anterior corneal dystrophies: preoperative and postoperative ultrasound biomicroscopic examination and short-term clinical outcomes with and without an antihyperopia treatment.

PURPOSE To evaluate the use of high-frequency ultrasound biomicroscopy (UBM) in determining the depth of corneal pathology in eyes undergoing excimer laser phototherapeutic keratectomy (PTK) for primary or recurrent anterior stromal corneal dystrophies. Corneal clarity, visual acuity and refractive changes in eyes with and without an antihyperopia treatment were also analyzed. METHODS Twenty eyes of 14 patients with anterior stromal corneal dystrophies were treated with PTK. Eyes were evaluated preoperatively and 6 to 8 weeks postoperatively with slit-lamp biomicroscopy, manifest refraction, keratometry, computerized corneal topography, ultrasound pachymetry, and UBM. RESULTS Nineteen of 20 corneas (95%) had greatly improved corneal clarity after PTK. Mean uncorrected Snellen vision improved from 20/102 to 20/69 and best corrected vision improved from 20/62 to 20/38. Nine eyes (45%) improved 2 or more lines of uncorrected vision, and 13 eyes (65%) improved 2 or more lines of best corrected vision. Mean change in spherical equivalent was just -0.92 diopters (D); however, the range was large (-13 to +3.88 D). UBM measurement of central corneal pathology did not correlate with the actual PTK ablation depth (P = .07). The amount of antihyperopia treatment did not correlate with changes in manifest refraction spherical equivalent, keratometry, or computerized corneal topography readings, but did correlate with length of time until corneal reepithelialization after PTK (P = .003). CONCLUSIONS PTK resulted in improvements in corneal clarity and visual acuity in most patients with superficial corneal stromal dystrophies. UBM was not an effective tool to accurately measure the depth of corneal pathology preoperatively. The combined approach of minimizing ablation depth and selective use of an antihyperopia treatment resulted in minimal mean change in spherical equivalent; however, the range was large. PTK is a very good minimally invasive technique to improve vision in eyes with anterior stromal corneal dystrophies.
RNA Scaffolds for Minihelix-Based Aminoacyl Transfer: Design of “Transpeptizymes”

Abstract Some evidence and considerations suggest that RNA minihelices based on the acceptor-TΨC stem-loop of tRNAs are the historical, more ancient part of the tRNA structure. These minihelices are substrates for aminoacylation by tRNA synthetases. In the transition from the RNA world to the theatre of proteins, aminoacyl minihelices may have had a role in early systems of peptide synthesis. Such systems would require bringing together aminoacyl groups into close proximity in order for peptide bonds to form. Here we report the design of RNA scaffolds based on pieces of the structure of the P4-P6 domain of the Tetrahymena ribozyme. RNA minihelices were incorporated into these scaffolds and the resulting RNAs could be enzymatically aminoacylated. The RNA scaffolds containing the minihelix-like pieces associated spontaneously to create the presumptive P4-P6 structure and thereby bring together the substrates for aminoacylation. Thus, peptide synthesis with associating RNA scaffolds that contain minihelix-like motifs appears plausible.
Early adolescent outcomes for institutionally-deprived and non-deprived adoptees. I: disinhibited attachment.

BACKGROUND Disinhibited attachment is an important sequel of an institutional rearing, but questions remain regarding its measurement, its persistence, the specificity of the association with institutional rearing and on whether or not it constitutes a meaningful disorder. METHOD Children initially reared in profoundly depriving institutions in Romania and subsequently adopted into UK families were compared with respect to findings at 11 years with children who had not experienced institutional deprivation and who had been adopted within the UK before the age of 6 months. Measures included parental reports, a Strange Situation procedure modified for use in the home and systematic standardised investigator ratings of the children's behaviour. RESULTS Disinhibited attachment, as reported by parents, showed a high degree of persistence from 6 to 11, but also a reduction over time in its frequency. Investigator ratings validated the parental reports but suggested that much of the fall in rate of disinhibited attachment was a function of the parental measure being less developmentally appropriate at 11 than it had been at 6. Disinhibited attachment was strongly associated with institutional rearing but there was not a significant increase in relation to duration of institutional deprivation beyond the age of 6 months. Mild, but not marked, disinhibited attachment was quite frequent in non-institutionalised adopted children but both the course and correlates indicated that its meaning was probably quite different. In the institution-reared children, disinhibited attachment was associated with a marked increase in service usage and associations with other forms of psychopathology. CONCLUSIONS Disinhibited attachment constitutes a valid, and handicapping, clinical pattern that is strongly associated with an institutional rearing.
Differential role of superoxide and glutathione in S‐nitrosoglutathione‐mediated apoptosis: a rationale for mild forms of familial amyotrophic lateral sclerosis associated with less active Cu,Zn superoxide dismutase mutants

SH‐SY5Y cells transfected with the enzymatically inactive Cu,Zn superoxide dismutase mutant H46R were more resistant to S‐nitrosoglutathione (GSNO)‐induced apoptosis. Cytochrome c release from mitochondria, caspase 3 activation, p53 up‐regulation, p21 cleavage and Bcl‐2 modulation, all involved in the apoptotic process, were significantly less altered with respect to untransfected cells. The H46R resistance to NO was associated with a higher content of reduced glutathione (GSH) and was abolished by blockage of glutathione synthesis. On the other hand, H46R cells were as sensitive as SH‐SY5Y cells to puromycin‐induced apoptosis; furthermore, they were more susceptible to apoptosis elicited by the superoxide‐generating drug paraquat and to cell necrosis provoked by t‐butyl hydroperoxide. These results confirm that the level of superoxide dismutase activity is fundamental for protecting cells against oxygen free radical challenge. Its impairment is not detrimental to cells exposed to NO, as long as the overall reducing power represented by GSH is assured. These results are relevant to explain a milder progression of the familial amyotrophic lateral sclerosis disease when associated with the H46R mutation.