Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutation detection in KRAS Exon 1 by constant denaturant capillary electrophoresis in 96 parallel capillaries.

Mutations in KRAS exon 1 oncogene are frequently found in colon carcinomas. A correlation between the mutated KRAS and the prognosis and outcome of treatment of colon cancer patients was reported in the literature. The object of our work was to establish a high-throughput method with high sensitivity to enable screening of tumor mutation status of KRAS exon 1 in large groups of colon cancer patients. KRAS exon 1 sequences from DNA isolated from 191 sporadic colon cancers were PCR amplified using one primer labeled with fluorescein and a second primer extended by a GC-clamp. After PCR amplification samples were subjected to automated 96-array constant denaturant capillary electrophoresis using a modified MegaBACE 1000 sequencing instrument. Mutant samples were identified by characteristic peak patterns. The sensitivity of detection of a mutant allele in a background of the wild-type alleles was 0.3%. Using the 96-array instrument a typical screening of 191 samples for KRAS mutation status could be performed within 2 h. A KRAS exon 1 mutation was found in 66 of 191 (34.6%) of the samples. The 96-array constant denaturant capillary electrophoresis provides an opportunity for the high-sensitivity screening of large cancer populations for KRAS exon 1 mutations.
Integral and transformative engineering coursework in formative research for undergraduate curricula

At several private Peruvian universities, formative research was not included in the curricula design. Here the problem to solve was the small number of undergraduate dissertations in Engineering. First, the coursework design and tutoring were reviewed and reformulated. The former proposal was based on the triangle of Peñaloza Ramella, in this study, this view was extended to a double triangle. The proposed extension uses an inverted triangle in order to compensate for the insufficient preparation in high school. Second, problems were identified comparing current outcomes against the desired undergraduate dissertations. The design used a mix of the transformative research ideas at US education institutions and the triangle's formulation of Peñaloza-Ramella, where the first triangle is to assure student preparation for different ways of formative research and the second one is to adapt the coursework to the original triangle to get more specific results each semester. Furthermore, several aspects in the use of resources were promoted (e.g. use of IEEE Xplore databases). In the first year, results have shown (1) acceptance by former students (before academic semester 2014-2) of these changes, generating 12 dissertations, (2) a change in few courses in formative research clearly enhanced at semesters II, III and VII, (3) an increase in the number of undergraduate dissertations during coursework, (4) first works accepted and presented in a Peruvian Student Competition Congress (5) all alumni with professional degrees have completed their undergraduate dissertation. Finally, in the next four years, a new generation of students is going to emerge with a significant improvement of their quality and their reasoning skills.
Acute to chronic ratios in aquatic toxicity—variation across trophic levels and relationship with chemical structure

For fish, daphnids, and algae, acute to chronic ratios (ACRs) have been determined from experimental data regarding new and existing chemicals. Only test results in accord with the European Union Technical Guidance Document (TGD) and validated by authorities were considered. Whereas the median ACRs of 10.5 (fish), 7.0 (daphnids), and 5.4 (algae) are well below the ACR safety factor of 100 as implied by the TGD, individual ACRs vary considerably and go up to 4,400. The results suggest that a safety factor of 100 is not protective for all chemicals and trophic levels. Neither a correlation between ACR and baseline toxicity as modeled through the logarithmic octanol–water partition coefficient nor an ACR correlation across trophic levels exists. Narcosis is associated with a preference for a low ACR; nevertheless, low ACRs are frequently obtained for nonnarcotics. Analysis of chemical structures led to the derivation of structural alerts to identify compounds with a significantly increased potential for a high ACR, which may prove to be useful in setting test priorities. At present, however, life‐cycle tests are the only way to conservatively predict long‐term toxicity.
Evaluation of Urinary S100B Protein Level and Lactate/Creatinine Ratio for Early Diagnosis and Prognostic Prediction of Neonatal Hypoxic-Ischemic Encephalopathy

Background: Early identification and prevention of hypoxic-ischemic encephalopathy (HIE) in newborns may reduce neonatal mortality and neurological dysfunction. Objective: To analyze the diagnostic and prognostic values of urinary S100B level and lactate/creatinine ratio in newborns with HIE. Methods: Seventy-eight full-term newborns with HIE and 25 normal newborns were enrolled. The Neonatal Behavioral Neurological Assessment (NBNA) and Developmental Screening Test were scored. The concentration of urinary S100B protein was determined using the S100B enzyme-linked immunosorbent assay and the levels of urinary lactate and creatinine were measured with the enzyme colorimetric method. Results: Urinary S100B level on days 1–3 after birth and lactate/creatinine ratio on day 1 were significantly higher in newborns with HIE than those in the control group. Both indexes were positively correlated with the clinical grading of HIE. A cutoff value for the S100B level of 0.47 μg/l on day 3 after birth had a sensitivity of 90% and specificity of 92% for prediction of HIE. A lactate/creatinine ratio of more than 0.55 on day 1 showed the highest sensitivity (92%) and specificity (90%). A combination of both indexes improved the sensitivity and specificity to 99 and 97%, respectively. A negative correlation of both lactate/creatinine ratio on day 1 and S100B level on days 1–3 after birth with the NBNA score was identified on days 3, 7 and 14 after birth. The Developmental Screening Test score of 36 newborns with HIE within 6 months after birth showed that 65% of infants with moderate and high HIE had an abnormal developmental quotient. Conclusion: These data suggest that early measurement of both S100B level and lactate/creatinine ratio in the urine of newborns with HIE is a practical convenient and sensitive way to improve diagnosis on the third day of life and prognostic prediction of HIE.
Critical determinants of host receptor targeting by Neisseria meningitidis and Neisseria gonorrhoeae : identification of Opa adhesiotopes on the N‐domain of CD66 molecules

The human pathogens Neisseria meningitidis and Neisseria gonorrhoeae express a family of variable outer membrane opacity‐associated (Opa) proteins that recognize multiple human cell surface receptors. Most Opa proteins target the highly conserved N‐terminal domain of the CD66 family of adhesion molecules, although a few also interact with heparan sulphate proteoglycans. In this study, we observed that at least two Opa proteins of a N. meningitidis strain C751 have the dual capacity to interact with both receptors. In addition, all three Opa proteins of C751 bind equally well to HeLa cells transfected with cDNA encoding the carcinoembryonic antigen [CEA (CD66e)] subgroup of the CD66 family, but show distinct tropism for CGM1‐ (CD66d) and NCA (CD66c)‐expressing cells. Because the C751 Opa proteins make up distinct structures via the surface‐exposed hypervariable domains (HV‐1 and HV‐2), these combinations appear to be involved in tropism for the distinct CD66 subgroups. To define the determinants of receptor recognition, we used mutant proteins of biliary glycoprotein [BGP (CD66a)] carrying substitutions at several predicted exposed sites in the N‐domain and compared their interactions with several Opa proteins of both N. meningitidis and N. gonorrhoeae. The observations applied to the molecular model of the BGP N‐domain that we constructed show that the binding of all Opa proteins tested occurs at the non‐glycosylated (CFG) face of the molecule and, in general, appears to require Tyr‐34 and Ile‐91. Further, efficient interaction of distinct Opa proteins depends on different non‐adjacent amino acids. In the three‐dimensional model, these residues lie in close proximity to Tyr‐34 and Ile‐91 at the CFG face, making continuous binding domains (adhesiotopes). The epitope of the monoclonal antibody YTH71.3 that inhibits Opa/CD66 interactions was also identified within the Opa adhesiotopes on the N‐domain. These studies define the molecular basis that directs the Opa specificity for the CD66 family and the rationale for tropism of the Opa proteins for the CD66 subgroups.
Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.
Transient ischemic attack with infarction: A unique syndrome?

It is debated whether transient symptoms associated with infarction (TSI) are best considered a minor ischemic stroke, a subtype of transient ischemic attack (TIA), or a separate ischemic brain syndrome. We studied clinical and imaging features to establish similarities and differences among ischemic stroke, TIA without infarction, and TSI. Eighty‐seven consecutive patients with TIA and 74 patients with ischemic stroke were studied. All underwent diffusion‐weighted imaging on admission. Symptom duration and infarct volume were determined in each group. Thirty‐six patients (41.3%) with TIA had acute infarct(s). Although TIA‐related infarcts were smaller than those associated with ischemic stroke (mean, 0.7 vs 27.3ml; p < 0.001), there was no lesion size threshold that distinguished ischemic stroke from TSI. In contrast, the symptom duration probability density curve was not broad, but instead peaked early with only a few patients having symptoms for longer than 200 minutes. The probability density function for symptom duration was similar between TIA with or without infarction. The in‐hospital recurrent ischemic stroke and TIA rate was 19.4% in patients with TSI and 1.3% in those with ischemic stroke. TIA with infarction appears to have unique features separate from TIA without infarction and ischemic stroke. We propose identifying TSI as a separate clinical syndrome with distinct prognostic features. Ann Neurol 2005;57:679–686
The conserved N‐terminal BH4 domain of Bcl‐2 homologues is essential for inhibition of apoptosis and interaction with CED‐4

Bcl‐2 and close homologues such as Bcl‐xL promote cell survival, while other relatives such as Bax antagonize this function. Since only the pro‐survival family members possess a conserved N‐terminal region denoted BH4, we have explored the role of this amphipathic helix for their survival function and for interactions with several agonists of apoptosis, including Bax and CED‐4, an essential regulator in the nematode Caenorhabditis elegans. BH4 of Bcl‐2 could be replaced by that of Bcl‐x without perturbing function but not by a somewhat similar region near the N‐terminus of Bax. Bcl‐2 cell survival activity was reduced by substitutions in two of ten conserved BH4 residues. Deletion of BH4 rendered Bcl‐2 (and Bcl‐xL) inactive but did not impair either Bcl‐2 homodimerization or ability to bind to Bax or five other pro‐apoptotic relatives (Bak, Bad, Bik, Bid or Bim). Hence, association with these death agonists is not sufficient to promote cell survival. Significantly, however, Bcl‐xL lacking BH4 lost the ability both to bind CED‐4 and antagonize its pro‐apoptotic activity. These results favour the hypothesis that the BH4 domain of pro‐survival Bcl‐2 family members allows them to sequester CED‐4 relatives and thereby prevent apoptosis.
Evaluation of bone mineral density, bone metabolism, osteoprotegerin and receptor activator of the NFkappaB ligand serum levels during treatment with infliximab in patients with rheumatoid arthritis.

OBJECTIVES To examine whether treatment with anti-tumour necrosis factor (TNF) alpha prevents loss of bone mineral density (BMD) at the spine and hip (generalised) and in the hands (local) of patients with rheumatoid arthritis, and to study the changes in markers of bone metabolism, including receptor activator of the NFkappaB ligand (RANKL) and osteoprotegerin (OPG), during anti-TNF treatment. PATIENTS AND METHODS 102 patients with active rheumatoid arthritis, who were treated with infliximab during 1 year, were included in this open cohort study. The BMD of the spine and hip (dual x ray absorptiometry) and hands dual x ray radiogrammetry was measured before the start of treatment and after 1 year. Changes in osteocalcin formation, beta-isomerised carboxy terminal telopeptide of type 1 collagen (beta-CTx, resorption), RANKL and OPG were determined at 0, 14, 30 and 46 weeks. RESULTS The BMD of the spine and hip was unchanged during treatment with infliximab, whereas BMD of the hand decreased significantly by 0.8% (p<0.01). The BMD of the hip in patients with a good European League Against Rheumatism response showed a favourable change compared with patients not achieving such a response. Serum beta-CTx and RANKL were both considerably decreased compared with baseline at all time points. The decrease in beta-CTx was associated with the decrease in Disease Activity Score of 28 joints and C reactive protein during the 0-14 weeks interval. CONCLUSION In patients with rheumatoid arthritis treated with infliximab, spine and hip bone loss is arrested, whereas metacarpal cortical hand bone loss is not stopped. The outcome of the study also supports a relationship between clinical response, in terms of reduced inflammatory activity, and changes in bone loss of the spine, hip and hands.
Lens With Transformable-Type and Tunable-Focal-Length Characteristics

A versatile lens with transformable-type and tunable-focal-length characteristics has been presented. The conventional punching technology is adopted to fabricate the lens structure due to its inherently high direction-holding capability. As a result, the alignment between two ends of the lens can be easily achieved without requiring complicated process. At the same time, soft lithography is used to realize structure similar to liquid-filled lens except the working medium being air rather than liquid acting as a tuning mechanism. These two parts are eventually combined together with bonding under oxygen plasma activation. With this design, large flexibility in performance tuning will be added to the lens, which has been experimentally demonstrated in beam shaping and imaging applications.
Growth and Pathogenesis of Mycoplasma mycoides var. capri in Chicken Embryo Tracheal Organ Cultures

The growth and pathogenicity of Mycoplasma mycoides var. capri were studied in chicken embryo tracheal rings in rolled tubes. In these organ cultures, M. mycoides var. capri attained titers of 107 to 108 color-changing units/ml of Eagle's medium and there was inhibition of ciliary activity. The rapidity of inhibition was directly related to the number of organisms inoculated. Growth of organisms was closely associated with the tracheal tissue because multiplication was not demonstrated in “conditioned medium,” that is Eagle's medium from which the rings had been removed. Mycoplasma growth occurred when the cultures were incubated at 37 C, 33 C, and room temperature, but the cilia-stopping effect (CSE) was most rapid at 37 C and was not demonstrable at room temperature. Furthermore, there was no CSE when cultures were maintained in medium in which M. mycoides var. capri had been grown but was either filtered to remove the organisms or treated with tetracycline to stop their multiplication. This indicated that the CSE of M. mycoides var. capri was dependent upon a close association of multiplying organisms with the tracheal rings and was not due to toxic products persisting in the medium. Chicken tracheal epithelial cells did not adsorb to colonies of M. mycoides var. capri but HeLa cells did. Although their adsorption was unaffected by prior neuraminidase treatment, the addition of neuraminidase to the tracheal organ culture system delayed the CSE of M. mycoides var. capri. Peroxide production was demonstrated in M. mycoides var. capri-infected tracheal rings but not in uninfected cultures. The addition of glucose to the organ cultures delayed the CSE of M. mycoides var. capri, possibly because of the stimulation of peroxidase activity. Similarily, catalase protected the cilia from the usual damaging effect of M. mycoides var. capri. This protective effect was partially reversed by the addition of 3-amino-1, 2, 4,-triazole and it did not occur if the catalase had been inactivated by boiling. The addition of hydrogen peroxide to tracheal cultures also resulted in loss of ciliary activity. The present results show that the liberation of peroxide is an important factor in the pathogenesis of M. mycoides var. capri infection of chicken tracheal organ cultures. It is speculated that this also may be so in the natural host.
Battle Management Language as a “Lingua Franca” for situation awareness

Information for situation awareness and management comes from a variety of sources, both device-generated (e.g., sensors) and human-generated. The latter includes databases, ontologies, intelligence reports, open source such as newspaper or television, and, increasingly informal communications such as Twitter or Facebook. Problematic is the fact that all of this information is created or stored in different formats, requiring processing and synthesis by humans. Furthermore, in international settings such as coalition operations, information may be in more than one natural language. Each of these factors makes automatic processing of information difficult, adding complexity and reducing timeliness. Battle Management Language offers a vehicle for automatic processing of information from diverse sources through a standardized representation, which preserves semantic information, while supporting information fusion and situation management.
In vivo screening of four phytochemicals/extracts and a fungal immunomodulatory protein against an Eimeria acervulina infection in broilers

Background: Besides the anticoccidial drug resistance problem, increasing consumer concerns about food safety and residues have propelled the quest for alternative prevention and control strategies amongst which phytotherapy has gained appeal due to a renewed interest in natural medicine.Objective: The objective was in vivo screening of four phytochemicals/extracts and a fungal immunomodulatory protein (FIP) against an Eimeria acervulina infection in broilers.Animals and methods: Four phytochemicals/extracts (extract from Echinacea purpurea, betaine (Betain™), curcumin, carvacrol (two different doses)), and a recombinant FIP from Ganoderma lucidum cloned and expressed in Escherichia coli were investigated for their anticoccidial potential. The experiment was conducted in a battery cage trial with 54 cages of eight birds each. Broilers infected with E. acervulina (a low and high infection dose of 104 and 105 sporulated oocysts, respectively) and treated with the phytochemicals/extracts or the FIP were compared with broilers treated with the anticoccidial salinomycin sodium (Sacox®) and with an untreated uninfected and an untreated infected control group. Coccidiosis lesion scores, body weight gains and oocyst shedding were used as parameters.Results: The results showed a coccidiosis infection dose effect on the mean coccidiosis lesion scores. The phytochemicals/extracts and the FIP failed to reduce coccidiosis lesion scores and oocyst shedding, while salinomycin efficiently controlled the E. acervulina infection and enabled significantly higher body weight gains.Conclusion: In conclusion, the selected phytochemicals/extracts and the FIP did not reduce the lesions of an experimentally induced E. acervulina infection.
A 0.13-$\mu{\rm m}$ CMOS Low-Power Capacitor-Less LDO Regulator Using Bulk-Modulation Technique

In this paper, a bulk-modulation technique is introduced for improving the performance of low-drop-out (LDO) voltage regulators. Compared to conventional LDO voltage regulators, the proposed circuit achieves improved accuracy, stability, and output load current capability. The technique is particularly suited for low-power applications such as biomedical implants and portable devices. A proof-of-concept prototype is designed and fabricated in 0.13-μm CMOS, to illustrate the enhancement that can be achieved by applying this technique. The proposed enhanced LDO regulator which is based on conventional LDO regulators is able to delivers up to 5 mA of load current while providing a 1 V (~ 1.5% load regulation) drawing 99.0 μA from a 1.2 V supply. Measurement results confirm that as compared to conventional LDOs, the proposed circuit offers better stability as well as %75 improvement in the load current delivery and ~10× faster recovery time for no-load to and from full-load transitions.
Donor leucocyte transfusions for relapse in myelodysplastic syndrome after allogeneic bone marrow transplantation

A 31‐year‐old man with refractory anaemia of excess blasts, which had karyotypic abnormalities, received an allogeneic bone marrow transplant (BMT). At time of relapse, 3 months after BMT, he was treated with donor leucocyte transfusions (DLT). Grade III acute GVHD (graft‐versus‐host disease) occurred 35 d after DLT which was fully reversed with cyclosporin and prednisolone. His condition was complicated by a herpes zoster infection. 2 months after DLT, neutrophil and platelet count were increased and karyotypic abnormalities disappeared. This observation demonstrates that DLT is an effective treatment for relapse of myelodysplastic syndrome (MDS) after BMT.