Targeted next-generation sequencing of circulating-tumor DNA for tracking minimal residual disease in localized colon cancer

BACKGROUND

A high percentage of patients diagnosed with localized colon cancer (CC) will relapse after curative treatment. Although pathological staging currently guides our treatment decisions, there are no biomarkers determining minimal residual disease (MRD) and patients are at risk of being undertreated or even overtreated with chemotherapy in this setting. Circulating-tumor DNA (ctDNA) can to be a useful tool to better detect risk of relapse.

PATIENTS AND METHODS

One hundred and fifty patients diagnosed with localized CC were prospectively enrolled in our study. Tumor tissue from those patients was sequenced by a custom-targeted next-generation sequencing (NGS) panel to characterize somatic mutations. A minimum variant allele frequency (VAF) of 5% was applied for variant filtering. Orthogonal droplet digital PCR (ddPCR) validation was carried out. We selected known variants with higher VAF to track ctDNA in the plasma samples by ddPCR.

RESULTS

NGS found known pathological mutations in 132 (88%) primary tumors. ddPCR showed high concordance with NGS (r = 0.77) for VAF in primary tumors. Detection of ctDNA after surgery and in serial plasma samples during follow-up were associated with poorer disease-free survival (DFS) [hazard ratio (HR), 17.56; log-rank P = 0.0014 and HR, 11.33; log-rank P = 0.0001, respectively]. Tracking at least two variants in plasma increased the ability to identify MRD to 87.5%. ctDNA was the only significantly independent predictor of DFS in multivariable analysis. In patients treated with adjuvant chemotherapy, presence of ctDNA after therapy was associated with early relapse (HR 10.02; log-rank P < 0.0001). Detection of ctDNA at follow-up preceded radiological recurrence with a median lead time of 11.5 months.

CONCLUSIONS

Plasma postoperative ctDNA detected MRD and identified patients at high risk of relapse in localized CC. Mutation tracking with more than one variant in serial plasma samples improved our accuracy in predicting MRD.

Olive oil mill effluents as a feedstock for production of biodegradable polymers

The aim of the present paper was to study the feasibility of using olive oil mill effluents (OMEs) as a substrate in biodegradable polymer production. OMEs were anaerobically fermented to obtain volatile fatty acids (VFAs), which are the most highly used substrate for polyhydroxyalkanotes (PHAs) production. The anaerobic fermentation step was studied both without pretreatment and with different pretreatments (i.e., centrifugation, bentonite addition, and bentonite addition followed by centrifugation) and at various concentrations (28.5, 36.7 and 70.4 g CODL(-1)). During fermentation, VFA concentration was determined (7-16 g CODL(-1)) as well as the corresponding yield with respect to initial COD (22-44%). At all initial concentrations, centrifugation pretreatment (with or without previous addition of bentonite) significantly increased the final VFA concentration and yield, whereas the addition of bentonite alone had no influence. Moreover, centrifugation pretreatment led to a different acid distribution, which affected the hydroxyvalerate (HV) content within the obtained copolymer poly beta-(hydroxybutyrate-hydroxyvalerate) [P(HB-HV)]. OMEs were tested for PHA production by using a mixed culture from an aerobic SBR. Centrifuged OMEs, both with or without fermentation, were tested. PHAs were produced from both matrices, but with fermented OMEs PHA production was much higher, because of the higher VFA concentration. The initial specific rate of PHA production obtained with fermented OMEs was approximately 420 mg COD g COD(-1)h(-1) and the maximum HV content within the copolymer was about 11% (on a molar basis). The HV monomer was produced only until propionic acid remained present in the medium.

Intrauterine contraception in nulligravid vs parous women

The performance of MLCu-250 IUDs inserted in 525 nulligravid women was studied for four years and is compared to the results obtained in the same period from 2770 parous women using TCu-200, 7Cu-200 and Nova-T IUDs. In every case the choice of the particular IUD model took into account hysterometry and diameter of the inner cervical orifice in order to aim at the highest theoretical efficacy. The MLCu-250 in nulligravid women produced failure and expulsion rates below those of the other models in parous users; no difference was observed in the case of removal because of bleeding or pain. Finally, there was no case of subsequent infertility or pelvic inflammatory disease (PID) recorded among nulliparae. These results suggest that an adequate choice of the IUD model for nulliparous women with low risk of PID gives as reliable results as in multiparous women.

Neurocysticercosis: optimal dose treatment with albendazole

Albendazole has been used successfully in the treatment of cerebral cysticercosis for several years. The published dosage schedule has varied from 15 mg/kg/day for 8 days to up to 30 days. Fifty three patients with neurocysticercosis received 8, 15 or 30 days treatment with 800 mg of albendazole daily. The present study demonstrates the effectiveness in clinical and radiological terms of albendazole 800 mg/day for 8 days for the majority of patients affected with cystic or encephalitic parenchymatous cysticercosis. There was no apparent advantage of continuation of treatment for 15 or 30 days in this series. The routine use of high dose steroids limited the effects of parasite destruction. No toxicity attributable to albendazole was encountered.

Kidney transplantation complications related to psychiatric or neurological disorders

Defining absolute psychiatric or neurological contraindications among kidney transplantation candidates is controversial, especially taking into account that graft outcomes are similar to other groups of patients. The social support network should be exhaustively evaluated to ensure adherence to immunosuppressive therapy and minimization of complications resulting from the neuropsychiatric disorder. We reviewed transplants (n = 668) in our center between January 2001 and August 2008 searching for patients with a diagnosis of neurological or psychiatric disease before renal transplantation. We also reviewed demographic data, social support networks, patient and graft survivals as well as transplant complications. Twelve patients were transplanted with neurological or psychiatric disorders: seven with cognitive impairment and five with psychiatric diseases. Nine patients had good social support networks. The mean follow-up time was 2.65 +/- 2.42 years. The graft loss rate was 34% (n = 4), including only one attributed to a mental disorder, namely, nonadherence to immunosuppressive therapy. Regarding complications, four were related to the neuropsychiatric disorder: hypoglycemia due to insulin overdose, aspiration pneumonia because of altered pharynx-larynx motility, hyponatremia related to diuretic abuse, and malnutrition plus dehydration. Patient survival in this period was 91.7%. The one patient died due to multiple organ failure secondary to respiratory sepsis with a functioning graft. In summary, neuropsychiatric disorders should not be considered to be contraindications for kidney transplantation although a social support network is essential and must be carefully evaluated.

Man-portable laser-induced breakdown spectroscopy system for in situ characterization of karstic formations

This paper reports the development and field testing of a man-portable instrument based on laser-induced breakdown spectrometry (LIBS) for inspection and analysis of speleothems. The 50 mJ of a Q-switched Nd:YAG laser operating at 1064 nm was used to generate a plasma on the sample. Plasma emission was then guided using a fiber-optic cable to a 1/10 m spectrometer equipped with a charge-coupled device (CCD) array detector. Plasma light was automatically processed in order to obtain surface and in-depth information from the speleothems. A field campaign in the interior of Nerja Cave (a large karstic formation in the South of Spain) has been carried out, aimed at evaluating the analytical performance of the instrument when operating in an unfriendly environment. Identification analysis of the speleothems' alteration layers and depth profiles of Sr and Ca is carried out and reported.

Highlighting the importance of transitional ventilation regimes in the management of Mediterranean show caves (Nerja-Pintada system, southern Spain)

This study shows the utilization of the air CO₂ exhaled by a very high number of visitors in the Nerja Cave as both a tracer and an additional tool to precisely evaluate the air circulation through the entire karst system, which includes non-touristic passages, originally free of anthropogenic CO₂. The analysis of the temporal - spatial evolution of the CO₂ content and other monitoring data measured from January 2015 to December 2016 in the Nerja-Pintada system, including air microbiological controls, has allowed us to define a new general ventilation model, of great interest for the conservation of the subterranean environment. During the annual cycle four different ventilation regimes and two ventilation modes (UAF-mode and DAF-mode) exist which determine the significance of the anthropogenic impact within the caves. During the winter regime, the strong ventilation regime and the airflow directions from the lowest to the highest entrance (UAF-mode) contribute to the rapid elimination of anthropogenic CO₂, and this affects the whole karstic system. During the summer regime the DAF-mode ventilation (with airflows from the highest to the lowest entrances) is activated. Although the number of visitors is maximum and the natural ventilation of the karstic system is the lowest of the annual cycle, the anthropogenic impact only affects the Tourist Galleries. The transitional ventilation regimes -spring and autumn- are the most complex of the annual cycle, with changing air-flow directions (from UAF-mode to DAF-mode and vice versa) at diurnal and poly diurnal scale, which conditions the range of the anthropogenic impact in each sector of the karst system. The activation of the DAF-mode has been observed when the temperature difference between the external and air cave is higher than 5°C.

[Evolution of the intake and nutritional status of zinc, iron and copper in women undergoing bariatric surgery until the second year after surgery]

INTRODUCTION

Bariatric surgery allows a significant reduction in weight and improvement of comorbidities associated with obesity in the long term, but it can also adversely affect the nutritional status of some micronutrients.

OBJECTIVES

To evaluate changes in intake and parameters of nutritional status of zinc, iron and copper in patients undergoing Roux-en-Y gastric bypass (GBP) or sleeve gastrectomy (SG), until the second postoperative year.

METHODS

We prospectively studied 45 women undergoing GBP or SG (mean age 35.2 ± 8.4 years, mean BMI 39.8 ± 4.0 kg/m²), every 6 months We measured intake and status indications nutritional zinc, iron and copper, and annually evaluated body composition. The contribution of minerals through supplements represented twice the recommended intake for a healthy woman in patients undergoing GT and three times for GBP.

RESULTS

20 women underwent GBP and 25 SG. In both groups there was a significant reduction in weight and body fat percentage, which was maintained until the second postoperative year. Women who have had a greater commitment GBP nutritional status of zinc, iron and copper, that patients undergoing SG.

CONCLUSIONS

Gastric bypass Roux-Y produces a greater commitment of nutritional status of zinc, iron and copper sleeve gastrectomy. It should evaluate whether administration of supplementation fractional improve the absorption of these nutrients.

Effect of IR laser radiation on germ cell DNA content after one cycle of the seminiferous epithelium

The effect of IR laser radiation on rat germ cells was investigated by cytophotometric quantification of the nuclear DNA content after a 15-day resting period. Two different doses of radiation energy were applied: 28.05 J/cm2 and 46.80 J/cm2. Both doses were found to increase the percentages of both spermatogonia with a 4c DNA content and primary spermatocytes with a > 4c DNA content. The elongating and elongated spermatids had a c DNA nuclear content, except for a small proportion (5%) of elongating cells that displayed a 2c DNA content at 28.05 J/cm2. Results revealed an increase in the germ cell DNA content after one cycle of the seminiferous epithelium after in vivo exposure to IR laser light. The laser sensitivity of the germ cells appeared to be related to their stage of differentiation and to the radiation energy applied, and the spermatogonia were the most sensitive. In all cases the lowest dosage induced the highest alteration.

[Alopecia in women with severe and morbid obesity who undergo bariatric surgery]

INTRODUCTION

Bariatric surgery leads to a significant body weigh reduction although it is associated to a higher risk of presenting some nutritional deficiencies. A common complication, little studied and mainly related to zinc deficiency is alopecia.

OBJECTIVES

To compare the nutritional status of zinc, iron, copper, selenium and protein-visceral in women with different degrees of hair loss at 6 months after gastric bypass or tubular gastrectomy.

METHODS

The patients were categorized into two groups according to the degree of hair loss: group 1 or mild loss (n = 42) and group 2 or severe hair loss (n = 45). Zinc, iron, copper, and selenium, as well as the indicators of the nutritional status of zinc, iron, copper, and proteinvisceral were assessed before and after 6 months of the surgery.

RESULTS

In both groups there was a significant body weight reduction at 6 months post-surgery (-38.9% ± 16.4%). Patients in group 1 presented a significantly higher intake of zinc (20.6 ± 8.1 vs. 17.1 ± 7.7 mg/d) and iron (39.7 ± 35.9 vs. 23.8 ± 21.3 mg/d.), and lower compromise in the nutritional status of zinc and iron than group 2. However, patients in group 2 had lower compromise in the nutritional status of copper. There were no differences regarding the plasma concentrations of albumin.

CONCLUSIONS

The patients having lower hair loss at six months after surgery had higher zinc and iron intake and lower compromise of the nutritional status of both minerals.

Portal and mesenteric vein thrombosis in a patient heterozygous for a mutation (Arg506-->Gln) in the factor V gen (factor V Leiden)

In 30-50% of patients with portal thrombosis, no underlying etiology is found. The recent reports of new hereditary clotting defects are contributing to the understanding of this problem, but they only justify a small number of idiopathic cases. Instead, anticoagulant protein C resistance, caused by a mutation in the V factor gene, appears to be at least 10 times more common than any of the other known inherited deficiencies of anticoagulant proteins. In spite of that, extensive thrombosis of portomesenteric or hepatic venous circulation has been rarely described in this hereditary clotting defect. We report a typical case of familial and recidivant deep vein thrombosis in a young man heterozygous for the factor V Leiden mutation (Arg506-Gln), who developed an acute portal and mesenteric vein thrombosis. The patient was discharged with an oral anticoagulant treatment and remains asymptomatic 2 years later. In conclusion, the high prevalence of the factor V Leiden in young and aged patients with idiopathic vein thrombosis and the case here described makes it obligatory to consider this disorder in patients with portal and/or mesenteric vein thrombosis, especially in those without evident etiology.

Germ cell DNA quantification shortly after IR laser radiation

The immediate effect of IR laser radiation on rat germ cells was studied by cytophotometric quantification of the nuclear DNA content in testicular sections. Two different levels of radiation were studied: one according to clinical application (28.05 J/cm2) and another known to increase the germ cell number (46.80 J/cm2). The laser beam induced changes in the germ cell DNA content depending on the cell type, the cell cycle phase and the doses of radiation energy applied. Following irradiation at both doses the percentage of spermatogonia showing a 4c DNA content was increased, while the percentage of these with a 2c DNA content was decreased. Likewise, the percentages of primary spermatocytes with a DNA content equal to 4c (at 28.05 J/cm2), between 2c and 4c (at 46.80 J/cm2) and higher than 4c (at both doses) were increased. No change in the mean spermatid DNA content was observed. Nevertheless, at 46.80 J/cm2 the percentages of elongated spermatids with a c or 2c DNA content differed from the controls. Data show that, even at laser radiation doses used in therapy, the germ cell DNA content is increased shortly after IR laser radiation.

Importance of monitoring and treatment of failed maturation in radiocephalic arteriovenous fistula in predialysis: Role of ultrasound

The aim of the study was to analyse outcomes of AVF-RC in predialysis stage in which a clinical and radiological follow up of its maturation had been done and primary failure had been treated.

MATERIAL AND METHODS

We studied 127 RC-AVF in 117 predialysis patients. All cases had a preoperative map. The RC-AVF was considered mature if it had a brachial artery flow ≥500ml/min and a cephalic vein diameter of ≥4mm. Primary failure was treated radiologically or surgically depending on the type of lesion. Fifty-eight patients started dialysis at the time of the study.

RESULTS

In 106 RC-AVF without thrombosis, 72 (68%) were mature and 34 (32%) were immature. A total of 97% of the immature had at least one lesion, and the most common site was the post-anastomotic vein. Lesions were found in 31% of mature RC-AVF, and 18% of patients required treatment. Radiological treatment was the most frequent for maturation failure. After 6 months, primary and secondary patency were 59% and 78%, while after 12 months they were 48% and 77%, respectively. The 80% of patients started dialysis with a distal AVF (76% RC-AVF and 4% ulnar basilic). None of the patients with treated immature RC-AVF started dialysis with CVC, while 78% of the patients started with said AVF.

CONCLUSION

Ultrasonography for monitoring maturation provides advantages over clinical monitoring. With our management of RC-AVF in predialysis, 80% of patients start dialysis with an adequate distal AVF.

Coupling air temperature records and gravimetric data to interpret ventilation patterns in a Mediterranean karstic system (Nerja-Pintada caves, southern Spain)

Microclimate and geophysical studies are commonly applied to the characterization of karst systems although they are usually used separately. The main purpose of this manuscript is to show how the analysis of the data from both these research methods is a useful tool in the characterization of karst systems and we present the analysis of a specific case study: the Nerja- Pintada caves system. The joint analysis of the Nerja Cave and external air data (mainly temperatures) and the pre-existing gravimetric data of its surroundings (residual gravity anomaly map) have allowed us: 1) to postulate the existence of an unknown great cavity located near to the Nerja Cave and with direct influence in its ventilation and 2) to propose a new model of the Nerja-Pintada caves ventilation based on the changing connection between a "main cavity" system (Nerja Cave), with basically a transmissive function of airflows and an "annex cavities" sub-system, with different functioning as far as the airflow is concerned: transmissive in the case of Pintada Cave and capacitive in the case of the geophysically-located cave.

Gaseous contaminant emissions as affected by burning scrap tires in cement manufacturing

We studied the environmental impact (gaseous emissions) of using scrap tires as a fuel substitute at a cement plant that produces one million tons of cement per year. Using a combination of tires and coal as opposed to only coal caused variations in the pollutant emission rate. The study recorded a 37% increase in the rate of emission for CO, a 24% increase for SO2, an 11% decrease for NOx, and a 48% increase for HCl when tires were included. The rate of emission for metals increased 61% for Fe, 33% for Al, 487% for Zn, 127% for Pb, 339% for Cr, 100% for Mn, and 74% for Cu, and decreased 22% for Hg. On the other hand, the emission rate of organic compounds dropped by 14% for polycyclic aromatic hydrocarbons, 8% in naphthalene, 37% in chlorobenzene, and 45% in dioxins and furans. We used a Gaussian model of atmospheric dispersion to calculate the average pollutant concentration (1-h, 24-h, and annual concentrations) in the ambient air at ground level with the help of the ISC-ST2 software program developed by the USEPA. When tires were used, we observed (i) a 12 to 24% increase in particulate matter, this range considering the concentration variation depending on the average used (1-h, 24-h, and annual basis), 31 to 52% in CO, 22 to 34% in SO2, 39 to 52% in HCl, 12 to 27% in Fe, -3 to 8% in Al, 30 to 37% in Zn, and 270 to 885% in Pb; (ii) a decrease of 8 to 13% in NOx, 9 to 13% in polycyclic aromatic hydrocarbons, 6 to 7% in naphthalene, 32 to 39% in chlorobenzene, and 32 to 45% in dioxins and furans. The results obtained showed that the maximum ground-level concentrations were well within the environmental standards (for operation with only coal as well as for operation with a combination of coal and tires).

Acanthosis nigricans as an indicator of insulin resistance in Chilean adult population

BACKGROUND

Insulin resistance (IR) is associated with a higher risk of multiple diseases and its early detection would allow to minimize the associated risk; the presence of acanthosis nigricans (AN) it's associated to the presence of IR.

OBJECTIVE

To evaluate the sensibility and specificity of AN to diagnose IR in a group of Chilean patients.

METHODS

We designed a cross-sectional study and it was included subjects that were attended at the Center for the Attention of Metabolic Diseases at the Faculty of Medicine, University of Chile. Sixty subjects (18-60 years age) were included. It was determined BMI and diagnosed AN and skin phototype; blood samples were taken and calculated the HOMA-IR. The normality of the variables where analyzed by Kolmogorov-Smirnov test. There were used χ² and the diagnostic concordance between AN and IR was determined using the Kappa index and Pearson's correlation. Sensibility, specificity, positive and negative predictive value were calculated and accepted p<0.05.

RESULTS

The IR diagnose was 67% and AN was 43%. The major proportion of subjects diagnosed as positive for IR were also positive for AN (84.6%). The sensibility of AN to find IR was an 84% and specificity was 100%. Positive and negative predictive values were 100% and 89% respectively. It was observed a positive association between BMI and HOMA-IR (r=0.674; r²=0.454; p<0.001).

CONCLUSION

To detect acanthosis nigricans in Chilean population may be effective for the early diagnose of insulin resistance and, therefore, reduce the associated cost of the late treatment of glucose metabolic disturbances.

New methods of mathematical analysis for studies of intrauterine contraception

The authors present two new procedures of mathematical analysis to evaluate the incidents which arise during the use of any contraceptive method. These two new approaches, which the authors call the Probability Index (PI) and the Weighted Average Index (WAI), are compared to those by Pearl and Tietze. Their conclusions are that the PI, although the best estimator of real probability, is not as functional as the WAI. The latter is not only much easier to calculate than PI, but also presents a greater correlation, prediction accuracy and discriminant power than the Pearl and Tietze indexes.

Identification of missing persons: the Spanish "Phoenix" program

In 1999, Spain was the first country to officially start a National Program to try to identify cadavers and human remains which could not be identified by the use of traditional forensic approaches. This attempt is called "Phoenix Program". Two independent mitochondrial DNA (mtDNA) databases were generated, which can automatically compare and match identical or similar sequences. One is the Reference Database, with mtDNA sequences from maternal relatives of missing persons, who provide the samples (buccal swabs) voluntarily; the other is the Questioned Database, comprised of mtDNA data of unknown remains and cadavers. Although the first phase of the program (typing of all unidentified human remains) will probably not be completed until December 2003, positive identifications are being made in the interim. To date, more than 1,200 families have contacted Phoenix, and at least 280 reference samples and 48 questioned evidences have been analyzed. When mtDNA matches are found, another independent analysis is performed as a part of the quality control mechanism. Once a match is confirmed (so far in 6 cases), an attempt is made to analyze short tandem repeat (STR) loci. We call for international collaboration to make this effort valuable worldwide.