The effect of chemical representation on active machine learning towards closed-loop optimization

Multivariate chemical reaction optimization involving catalytic systems is a non-trivial task due to the high number of tuneable parameters and discrete choices.

Comparison of Validity of Mapping between Drug Indications and ICD-10

Background: Mapping of drug indications to ICD-10 was undertaken in Korea by a public and a private institution for their own purposes. A different mapping approach was used by each institution, which presented a good opportunity to compare the validity of the two approaches.

Objectives: This study was undertaken to compare the validity of a direct mapping approach and an indirect terminology based mapping approach of drug indications against the gold standard drawn from the results of the two mapping processes.

Methods: Three hundred and seventy-five cardiovascular reference drugs were selected from all listed cardiovascular drugs for the study. In the direct approach, two experienced nurse coders mapped the free text indications directly to ICD-10. In the indirect terminology based approach, the indications were extracted and coded in the Korean Standard Terminology of Medicine. These terminology coded indications were then manually mapped to ICD-10. The results of the two approaches were compared to the gold standard. A kappa statistic was calculated to see the compatibility of both mapping approaches. Recall, precision and F1 score of each mapping approach were calculated and analyzed using a paired t-test.

Results: The mean number of indications for the study drugs was 5.42. The mean number of ICD-10 codes that matched in direct approach was 46.32 and that of indirect terminology based approach was 56.94. The agreement of the mapping results between the two approaches were poor (kappa = 0.19). The indirect terminology based approach showed higher recall (86.78%) than direct approach (p < 0.001). However, there was no difference in precision and F1 score between the two approaches.

Conclusions: Considering no differences in the F1 scores, both approaches may be used in practice for mapping drug indications to ICD-10. However, in terms of consistency, time and manpower, better results are expected from the indirect terminology based approach.

An examination of the elastic properties of tissue-mimicking phantoms using vibro-acoustography and a muscle motor system

Tissue hardness, often quantified in terms of elasticity, is an important differentiating criterion for pathological identity and is extensively used by surgeons for tumor localization. Delineation of malignant regions from benign regions is typically performed by visual inspection and palpation. Although practical, this method is highly subjective and does not provide quantitative metrics. We have previously reported on Vibro-Acoustography (VA) for tumor delineation. VA is unique in that it uses the specific, non-linear properties of tumor tissue in response to an amplitude modulated ultrasound beam to generate spatially resolved, high contrast maps of tissue. Although the lateral and axial resolutions (sub-millimeter and sub-centimeter, respectively) of VA have been extensively characterized, the relationship between static stiffness assessment (palpation) and dynamic stiffness characterization (VA) has not been explicitly established. Here we perform a correlative exploration of the static and dynamic properties of tissue-mimicking phantoms, specifically elasticity, using VA and a muscle motor system. Muscle motor systems, commonly used to probe the mechanical properties of materials, provide absolute, quantitative point measurements of the elastic modulus, analogous to Young's modulus, of a target. For phantoms of varying percent-by-weight concentrations, parallel VA and muscle motor studies conducted on 18 phantoms reveal a negative correlation (p < - 0.85) between mean signal amplitude levels observed with VA and calculated elastic modulus values from force vs. indentation depth curves. Comparison of these elasticity measurements may provide additional information to improve tissue modeling, system characterization, as well as offer valuable insights for in vivo applications, specifically surgical extirpation of tumors.

The occurrence of dystonia in upper-limb multiple sclerosis tremor

BACKGROUND

The pathophysiology of multiple sclerosis (MS) tremor is uncertain with limited phenotypical studies available.

OBJECTIVE

To investigate whether dystonia contributes to MS tremor and its severity.

METHODS

MS patients (n = 54) with and without disabling uni- or bilateral upper limb tremor were recruited (39 limbs per group). We rated tremor severity, writing and Archimedes spiral drawing; cerebellar dysfunction (SARA score); the Global Dystonia Scale (GDS) for proximal and distal upper limbs, dystonic posturing, mirror movements, geste antagoniste, and writer's cramp.

RESULTS

Geste antagoniste, mirror dystonia, and dystonic posturing were more frequent and severe (p < 0.001) and dystonia scores were correlated with tremor severity in tremor compared to non-tremor patients. A 1-unit increase in distal dystonia predicted a 0.52-Bain unit (95% confidence interval (CI) 0.08-0.97), p = 0.022) increase in tremor severity and a 1-unit (95% CI 0.48-1.6, p = 0.001) increase in drawing scores. A 1-unit increase in proximal dystonia predicted 0.93-Bain unit increase (95% CI 0.45-1.41, p < 0.001) in tremor severity and 1.5-units (95% CI 0.62-2.41, p = 0.002) increase in the drawing score. Cerebellar function in the tremor limb and tremor severity was correlated (p < 0.001).

CONCLUSIONS

Upper limb dystonia is common in MS tremor suggesting that MS tremor pathophysiology involves cerebello-pallido-thalamo-cortical network dysfunction.

Symptom differences and pretreatment asymptomatic interval affect outcomes of stenting for intracranial atherosclerotic disease

BACKGROUND AND PURPOSE

Different types of symptomatic intracranial stenosis may respond differently to interventional therapy. We investigated symptomatic and pathophysiologic factors that may influence clinical outcomes of patients with intracranial atherosclerotic disease who were treated with stents.

MATERIALS AND METHODS

A retrospective analysis was performed of patients treated with stents for intracranial atherosclerosis at 4 centers. Patient demographics and comorbidities, lesion features, treatment features, and preprocedural and postprocedural functional status were noted. χ(2) univariate and multivariate logistic regression analysis was performed to assess technical results and clinical outcomes.

RESULTS

One hundred forty-two lesions in 131 patients were analyzed. Lesions causing hypoperfusion ischemic symptoms were associated with fewer strokes by last contact [χ(2) (1, n = 63) = 5.41, P = .019]. Nonhypoperfusion lesions causing symptoms during the 14 days before treatment had more strokes by last contact [χ(2) (1, n = 136), 4.21, P = .047]. Patients treated with stents designed for intracranial deployment were more likely to have had a stroke by last contact (OR, 4.63; P = .032), and patients treated with percutaneous balloon angioplasty in addition to deployment of a self-expanding stent were less likely to be stroke free at point of last contact (OR, 0.60; P = .034).

CONCLUSIONS

More favorable outcomes may occur after stent placement for lesions causing hypoperfusion symptoms and when delaying stent placement 7-14 days after most recent symptoms for lesions suspected to cause embolic disease or perforator ischemia. Angioplasty performed in addition to self-expanding stent deployment may lead to worse outcomes, as may use of self-expanding stents rather than balloon-mounted stents.

Intracortical visual prosthesis research - approach and progress

Following the early work of Brindley in the late 1960's, the NIH began intramural and extramural funding for stimulation of the primary visual coretex using fine-wire electrodes that are inserted into area VI for the prupose of restoring vision in individuals with blindness. More recently researchers with experience in this projectbecame part of our multi-institutional team with the intention to identify and close technological gaps so that the intracortical approach might be tested in humans on a chronic basis. Our team has formulated an approach for testing a prototype system in a human volunteer. Here, we describe our progress and expectations.

Fragile X-associated tremor/ataxia phenotype in a male carrier of unmethylated full mutation in the FMR1 gene

The Fragile X syndrome is caused by a CGG repeat expansion >200 in the promoter of the Fragile X mental retardation 1 (FMR1) gene termed full mutation (FM). These alleles are silenced through methylation of the FMR1 promoter, leading to deficit of the FMR1 protein (FMRP), and neurodevelopmental changes. However, occasional FM individuals have a complete lack of methylation, and those typically have only minor deficit of FMRP levels compared with normal controls and their intelligence may be in the normal range. FM alleles are generated through expansion of the CGG repeat from the premutation (PM) range of 55-200 repeats, linked to the late onset Fragile X-associated tremor/ataxia syndrome (FXTAS). This disorder has been attributed to a 'toxicity' of the FMR1 mRNA, which is significantly elevated in male carriers of PM alleles and of unmethylated FM alleles. This is the first report of a 65-year-old male with an unmethylated FM allele and history of alcohol abuse, who developed symptoms of FXTAS. We postulate that, although the elevation of FMR1 transcripts associated with unmethylated FM alleles have a potential to cause FXTAS, in some cases this disorder may occur through an additional effect of exposure to neurotoxicants including alcohol.

Deleted in breast cancer 1 (DBC1) is a dynamically regulated protein

Deleted in breast cancer 1 (DBC1, KIAA1967, p30 DBC) is a novel protein that has been suggested to be a critical regulator of tumorigenesis. DBC1 modulates the activities of various proteins, including SIRT1, ERalpha, RARalpha, and AR. The functions of DBC1 with target molecules have been investigated, but little is known of its molecular characteristics. We found that DBC1 is homo-oligomerized and exhibits a dynamic expression pattern during cell cycle. In addition, DBC1 expression is higher in lung cancer cells than in normal lung fibroblasts and the protein recognized by anti-DBC1 antibodies in normal cells differs from that in lung and breast cancer cells. Further examination of the oligomerization and the dynamic expression of DBC1 during the cell cycle will help us to understand the mechanisms of DBC1 function. Moreover, the elucidation about differential expression of DBC1 between normal cells and cancer cells will aid the development of DBC1 as a diagnostic marker for cancers.

The salicylic acid-induced protection of non-climacteric unripe pepper fruit against Colletotrichum gloeosporioides is similar to the resistance of ripe fruit

The anthracnose fungus Colletotrichum gloeosporioides deleteriously affects unripe pepper fruit, but not ripe fruit. Here, we show that the induction of local acquired resistance (LAR) by salicylic acid (SA), 2,6-dichloroisonicotinic acid, or benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester pretreatment protects unripe pepper fruit against the fungus, while jasmonic acid (JA) does not. The SA-mediated LAR in the unripe fruit inhibited the fungal appressoria, resulting in protection against fungal infection. Microarray analysis revealed that 177 of 7,900 cDNA clones showed more than fourfold transcriptional accumulation in SA-treated unripe fruit. The reverse transcription-polymerase chain reaction showed that most of the SA-responsive genes (SRGs) were regulated by SA, but not by JA or ethylene-releasing ethephon. Furthermore, most of the SRGs were preferentially expressed in the ripe fruit. These results suggest that the SA-mediated transcriptional regulation of SRGs has a critical role in the resistance of ripe pepper fruit to fungal infection.

Predictive and prognostic functions of microtubule-associated protein-tau and topoisomerase IIα protein in early breast cancer

e22169

Background: Topoisomerase IIα protein(topo II) is the molecular target of topo II inhibitors such as anthracyclines and Microtubule-Associated Protein(MAP)-tau protein is associated with taxane sensitivity. Anthracyclins and taxanes are major cytotoxic agents of breast cancer in the adjuvant setting. The aim of this study was to evaluate the predictive and prognostic functions of MAP-tau and topo II in early breast cancers. Methods: Representative breast tumor sections were constructed from paraffin embedded specimens from 78 node positive breast cancer patients. MAP-tau and topo II protein were assessed by immunochemistry using antibody clone 4F1(Affinity BioReagents,USA) and clone Ki-S1 antibody(Dakocytomation,USA). MAP-tau staining of tumor cells was semiquantatively scored as 0, 1+, 2+, 3+ and cases with 0 or 1+ staining intensity were considered MAP-tau negative. Topo II protein over- expression was defined as the detection of nuclear staining in more than median value of evaluated cells. Results: Thirty- four cases (43.6%) of 78 samples showed topo II overexpression and 35 cases(44.9%) showed MAP-tau overexpression in node positive breast cancers. HER2 overexpression was noted in 28 samples (35.9%) and 56 cases (71.8%) were compatible with the luminal type. In 43 patients (55.1%), anthracyclin and taxane were used as adjuvant therapy and in this group, both MAP-tau and topo II overexpression showed lower disease-free survival (DFS) than the others, but statistically not significant. In luminal type, MAP-tau overexpression was poor prognostic factor on DFS in Cox regression.(HR 5.644, 95% CI 1.14–28.07, p=0.034) Conclusions: Topo II overexpression and MAP-tau overexpression in node positive breast cancers were not significant predictive factors for anthracyclin and taxane therapies. As several investigators reported, MAP-tau is associated endocrine therapy sensitivity in patients without chemotherapy, but higher MAP-tau in luminal type was a strong poor prognostic factor in patients who were given chemotherapy and hormonal therapy.

No significant financial relationships to disclose.

Hydrogen production by anaerobic microbial communities exposed to repeated heat treatments

Biological hydrogen production by anaerobic mixed communities was studied in laboratory-scale bioreactors using sucrose as the substrate. A bioreactor in which a fraction of the return sludge was exposed to repeated heat treatments performed better than a control bioreactor without repeated heat treatment of return sludge and produced a yield of 2.15 moles of hydrogen per mole of sucrose, with 50% hydrogen in the biogas. Terminal restriction fragment length polymorphism analysis showed that two different Clostridium groups (comprised of one or more species) were dominant during hydrogen production. The relative abundance of two other non-Clostridium groups increased during periods of decreased hydrogen production. The first group consisted of Bifidobacterium thermophilum, and the second group included one or more of Bacillus, Melissococcus, Spirochaeta, and Spiroplasma spp.

Anaerobic membrane bioreactor for treatment of synthetic municipal wastewater at ambient temperature

Non-woven fabric filter and poly-tetrafluoroethylene (PTFE) composite membrane were investigated to determine their applicability to treat low strength wastewater in an anaerobic membrane bioreactor (AMBR). Sludge cake resistance of the membrane was quantified using pure water flux of anaerobic sludge cake accumulated on the glass fiber filter of similar pore size. It is hypothesized that the formation of thin cake layer on the porous medium, e.g. non-woven and PTFE acts as a dynamic membrane. Thus, the capture of thin sludge cake inside the non-woven fabric matrix and accumulation on the PTFE membrane surface forms a membrane system equivalent to a commercial membrane system. The permeate quality was found to improve as the cake became more dense with filtration time. The PTFE composite membrane coated with thin PTFE film on the non-woven fabric filter enhanced the filtration performance by improving flux and minimizing the propensity of bio-fouling. The membrane flux was restored by back-flushing with permeate. The AMBR coupled with PTFE laminated membrane was operated continuously during the experiment at a cross flow velocity (CFV) of 0.1-0.2 m/sec and a transmembrane pressure (TMP) of 0.5-3 psi. Although about a month of acclimation was required to reach steady state, the effluent chemical oxygen demand (COD), volatile fatty acids (VFAs) as acetic acid, and suspended solids (SS) concentrations were below 30, 20 and 10 mg/L, respectively, during 90 days of operation with intermittent back washing. The lower operation TMP and CFV were subjected to less shear stress on the microbial community during continuous AMBR operation. In addition, thin sludge film accumulated on the membrane surface also acted as a biofilm bioreactor to remove additional COD in this study.

Adsorption of arsenic(V) by activated carbon prepared from oat hulls

The efficiency of self-manufactured activated carbon (AC) produced from oat hulls in adsorbing arsenic(V) was tested in a batch reactor. The results indicated that the adsorptive capacity of AC was affected by initial pH value, with adsorption capacity decreasing from 3.09 to 1.57 mg As g(-1) AC when the initial pH values increased from 5 to 8. A modified linear driving force model conjugated with a Langmuir isotherm was created to describe the study's kinetics. The test results show that rapid adsorption and slow adsorption exist simultaneously when AC is used to remove arsenic(V).

Enhanced brain levels of 8,12-iso-iPF2alpha-VI differentiate AD from frontotemporal dementia

OBJECTIVE

To quantify the isoprostane 8,12-iso-iPF2alpha-VI in brain tissues obtained from patients with AD, patients with frontotemporal dementia (FTD), and controls.

BACKGROUND

Enhanced brain oxidative stress with secondary damage to cellular macromolecules may play a role in the pathogenesis of AD and FTD. The isoprostane 8,12-iso-iPF2alpha-VI is a specific and sensitive marker of in vivo lipid peroxidation and is increased in AD.

METHODS

Levels of this isoprostane were determined by gas chromatography/negative ion chemical ionization mass spectrometry.

RESULTS

Levels of 8,12-iso-iPF2alpha-VI were markedly elevated in both frontal and temporal cortex of AD brains compared to the corresponding areas of FTD and controls. No significant difference in brain 8,12-iso-iPF2alpha-VI levels for any regions considered was observed between FTD and controls.

CONCLUSIONS

Lipid peroxidation is a feature of AD, but not FTD. The generation of 8,12-iso-iPF(2alpha)-VI in the brain is not a general or final common pathway of neurodegeneration, but may be relatively specific for disease processes in AD and not FTD.

Ammonia inhibition on thermophilic aceticlastic methanogens

The inhibition effects of total ammonia nitrogen (TAN) on aceticlastic methanogenic activity using biomass from thermophilic anaerobic reactors were investigated in this study. Anaerobic Toxicity Assays (ATA) were conducted after the biomass was acclimated to different levels of TAN. The TAN background concentrations in the reactors were 400, 1,200, and 3,050 mg/L. The results from ATA showed: 1) high TAN concentrations could cause inhibition of aceticlastic methanogens; 2) biomass acclimated to higher TAN concentrations could alleviate the inhibition effect due to the increase of TAN concentration; 3) the lethal TAN concentration for methanogens was approximately 10,000 mg/L regardless of the background TAN concentration; 4) ATA results also revealed the role played by pH. At a given TAN concentration, methanogenic activity varied with the pH values. The highest methanogenic activity was always observed at a pH of 7.0-7.5. 5) It was also observed that acclimation could increase the pH tolerance range, which made methanogens less sensitive to pH changes.

Biohydrogen production as a function of pH and substrate concentration

The conversion of organics in wastewaters into hydrogen gas could serve the dual role of renewable energy production and waste reduction. The chemical energy in a sucrose rich synthetic wastewater was recovered as hydrogen gas in this study. Using fractional factorial design batch experiments, the effect of varying pH (4.5-7.5) and substrate concentration (1.5-44.8 g COD/L) and their interaction on hydrogen gas production were tested. Mixed bacterial cultures obtained from a compost pile, a potato field, and a soybean field were heated to inhibit hydrogen-consuming methanogens and to enrich sporeforming, hydrogen-producing acidogens. It was determined that the highest rate (74.7 mL H2/(L*h)) of hydrogen production occurred at a pH of 5.5 and a substrate concentration of 7.5 g COD/Lwith a conversion efficiency of 38.9 mL H2/(g COD/L). The highest conversion efficiency was 46.6 mL H2/(g COD/L).

Palladium-catalyzed cross-coupling reactions of in situ generated allylindium reagents with aryl halides

[reaction: see text] In situ generated allylindium reagents from the reaction of 1 equiv of indium with 1.5 equiv of allyl halides could be effective cross-coupling partners in palladium-catalyzed cross-coupling reactions to aryl halides. The best results were obtained with 2% Pd(2)dba(3)CHCl(3) and 16% Ph(3)P in the presence of 3 equiv of LiCl in DMF at 100 degrees C.

Anaerobic migrating blanket reactor treatment of low-strength wastewater at low temperatures

The feasibility of the compartmentalized anaerobic migrating blanket reactor (AMBR) was studied for the treatment of low-strength soluble wastewater under low-temperature conditions. During an operating period of 186 days, a 20-L AMBR was fed nonfat dry milk substrate as a synthetic wastewater at low temperatures (15 and 20 degrees C). The concentration of the influent was constant at chemical oxygen demand (COD) and 5-day biological oxygen demand (BOD5) concentrations of 600 and 285 mg/L, respectively. The soluble COD (SCOD) removal efficiency was 73% at the end of the operating period (15 degrees C) at a 4-hour hydraulic retention time (HRT), while the total COD (TCOD) removal efficiency was 59%. At a 4-hour HRT, staged conditions promoted complete removal of propionic acid in the final compartments of the reactor. The specific methanogenic activity of granules increased slowly until the end of the operating time, improving the removal rate. Biomass was retained effectively, as evidenced by the solids retention time (SRT) that was always greater than 50 days even during step decreases of the reactor HRT from 12 hours to 4 hours. A long SRT also promoted system stability during changes in flow, which was observed by SCOD removal efficiencies staving greater than 70%. During a hydraulic stress test, the HRT was reduced from 4 hours to 1 hour for one day (24 HRTs) in which volatile suspended solids (VSS) in the effluent increased from an average background level of 8.7 g/d to 35 g/d and the SRT decreased from 50.5 days to 12.6 days. However, mixed liquor volatile suspended solids concentration decreased only by 1 g/L, and hence a similar COD removal efficiency and biogas production was found one day after the hydraulic stress (as compared to one day before the hydraulic stress).