Recent advances in clay minerals for groundwater pollution control and remediation.

Clay minerals are abundant on Earth and have been crucial to the advancement of human civilization. The ability of clay minerals to absorb chemicals is frequently utilized to remove hazardous compounds from aquatic environments. Moreover, clay-based adsorbent products are both environmentally acceptable and affordable. This study provides an overview of advances in clay minerals in the field of groundwater remediation and related predictions. The existing literature was examined using data and information aggregation approaches. Keyword clustering analysis of the relevant literature revealed that clay minerals are associated with groundwater utilization and soil pollution remediation. Principal component analysis was used to assess the relationships among clay mineral modification methods, pollutant properties, and the Langmuir adsorption capacity (Qmax). The results demonstrated that pollutant properties affect the Qmax of pollutants adsorbed by clay minerals. Systematic cluster analysis was utilized to classify the collected data and investigate the relationships. The pollution adsorption mechanism of the unique structure of clay minerals was investigated based on the characterization results. Modified clay minerals exhibited changes in surface functional groups, internal structure, and pHpzc. This review provides a summary of recent clay-based materials and their applications in groundwater remediation, as well as discussions of their challenges and future prospects.

Hydrogeochemical evolution of groundwater impacted by acid mine drainage (AMD) from polymetallic mining areas (South China).

Mining activities have long-term impacts on the groundwater of surrounding areas and deserve in-depth analysis and study. Herein, the geochemical mechanisms of acid mine drainage (AMD)-affected groundwaters were examined, and groundwater quality was assessed through water quality indices. 15 water samples from 7 domestic and 4 groundwater monitoring wells were tested for physical and chemical parameters in 2022, and multivariate statistical analysis was carried out with monitoring data from 21 domestic wells in 2010. The groundwater chemical composition varied from a predominantly Ca-HCO3 type in 2010 to a Ca-SO4 type in 2022. The isotopic values of δ18O and δD indicate that groundwater has not been significantly affected by evaporation. Changes in groundwater sulfate and total dissolved solids (TDS) levels over the twelve-year period confirmed the AMD infiltration impact on groundwater quality. The groundwater chemical properties changed more slowly than those of surface waters affected by AMD based on a cumulative increase in sulfate concentration of 29.94 mg/L. Changes in groundwater quality were investigated, namely, the spatiotemporal distribution of potentially toxic elements (PTEs), including Fe, Mn, Cd, Pb, and As. Mn concentrations in upstream groundwater areas near the mine decreased by 61.8% between 2010 and 2022. Conversely, groundwater in midstream areas had Mn concentrations of 2.25 mg/L and arsenic concentrations of 11.8 µg/L, both exceeding the WHO, 2022 standard. According to multivariate statistical analysis, Mn, Cd, and Pb originated from polymetallic minerals, whereas As was likely derived from the reduction of Fe/Mn hydroxyl oxides. AMD remediation improved contaminated upstream groundwater quality over 12 years, with a 36.8% improvement in WQI values. PTE distribution determined water quality changes; therefore, PTE contamination should be treated in mid- and downstream regions while contaminated groundwater should be treated upstream.

Immunogenicity and safety of BNT162b2 mRNA vaccine in Chinese adults: A phase 2 randomised clinical trial.

Background: BNT162b2, an mRNA vaccine against COVID-19, is being utilised worldwide, but immunogenicity and safety data in Chinese individuals are limited. Methods: This phase 2, randomised, double-blind, placebo-controlled trial included healthy or medically stable individuals aged 18-85 years enrolled at two clinical sites in China. Participants were stratified by age (≤55 or >55 years) and randomly assigned (3:1) by an independent randomisation professional to receive two doses of intramuscular BNT162b2 30 µg or placebo, administered 21 days apart. Study participants, study personnel, investigators, statisticians, and the sponsor's study management team were blinded to treatment assignment. Primary immunogenicity endpoints were the geometric mean titers (GMTs) of neutralising antibodies to live severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seroconversion rates (SCR) 1 month after the second dose. Safety assessments included reactogenicity within 14 days of vaccination, adverse events (AEs), and clinical laboratory parameters. Randomised participants who received at least one dose were included in the efficacy and safety analyses on a complete case basis (incomplete/missing data not imputed). Results up to 6 months after the second dose are reported. Findings: Overall, 959 participants (all of Han ethnicity) who were recruited between December 5th, 2020 and January 9th, 2021 received at least one injection (BNT162b2, n=720; placebo, n=239). At 1 month after the second dose, the 50% neutralising antibody GMT was 294.4 (95% CI; 281.1-308.4) in the BNT162b2 group and 5.0 (95% CI; 5.0-5.0) in the placebo group. SCRs were 99.7% (95% CI; 99.0%-100.0%) and 0% (95% CI; 0.0%-1.5%), respectively (p<0.0001 vs placebo). Although the GMT of neutralising antibodies in the BNT162b2 group was greatly reduced at 6 months after the second dose, the SCR still remained at 58.8%. BNT162b2-elicited sera neutralised SARS-CoV-2 variants of concern. T-cell responses were detected in 58/73 (79.5%) BNT162b2 recipients. Reactogenicity was mild or moderate in severity and resolved within a few days after onset. Unsolicited AEs were uncommon at 1 month following vaccine administration, and there were no vaccine-related serious AEs at 1 month or 6 months after the second dose. Interpretation: BNT162b2 vaccination induced a robust immune response with acceptable tolerability in Han Chinese adults. However, follow-up duration was relatively short and COVID-19 rates were not assessed. Safety data collection is continuing until 12 months after the second dose. Funding: BioNTech - sponsored the trial. Shanghai Fosun Pharmaceutical Development Inc. (Fosun Pharma) - conducted the trial, funded medical writing. ClinicalTrialsgov registration number: NCT04649021. Trial status: Completed.

Hormetic Effects of Dimethachlone on Mycelial Growth and Virulence of Sclerotinia sclerotiorum.

Fungicide hormesis has implications for the application of fungicides to control plant diseases. We investigated the hormetic effects of the dicarboximide fungicide dimethachlone on mycelial growth and virulence of the necrotrophic plant pathogen Sclerotinia sclerotiorum. Dimethachlone at sublethal doses in potato dextrose agar (PDA) increased the mycelial growth of S. sclerotiorum. After the growth-stimulated mycelia were subcultured on fresh PDA and inoculated on rapeseed leaves, increased mycelial growth and virulence were observed, indicating that hormetic traits were passed down to the next generation. Dimethachlone applied to leaves at 0.002 to 500 µg/ml stimulated virulence, with a maximum stimulation amplitude (MSA) of 31.4% for the isolate HLJ4, which occurred at 2 µg/ml. Dimethachlone-resistant isolates and transformants had a mean virulence MSA of 30.4%, which was significantly higher (P = 0.008) than the MSA for sensitive isolates (16.2%). Negative correlations were detected between MSA and virulence in the absence of any fungicide (r = -0.872, P < 0.001) and between MSA and mycelial growth on PDA (r = -0.794, P = 0.002). Studies on hormetic mechanisms indicated that dimethachlone had no significant effects on expression levels of three virulence-associated genes, that is, a cutinase-encoding gene SsCut, a polygalacturonase gene SsPG1, or an oxaloacetate acetylhydrolase gene SsOah1. The results will contribute to understanding hormesis and have implications for the judicious application of fungicides to control plant diseases.

An N-oxide-functionalized nanocage-based copper-tricarboxylate framework for the selective capture of C2H2.

The selective capture of C2H2 from C2H2-C2H4 and C2H2-CO2-CH4 mixtures is a very essential but highly challenging process during C2H4 and C2H2 purification in the chemical industry. In this work, by virtue of using oxygen-atom-rich C2H2 recognition sites, we, for the first time, designed and synthesized an N-oxide-functionalized tricarboxylate ligand and utilized it to successfully construct a copper-based MOF. N-Oxide functionalization exerted a significant effect on the ligand conformation, thus resulting in a new topological network that is different from that of the unoxidized parent compound. With a moderate surface area and the immobilization of N-oxide functionality and carboxylate oxygen atoms in two nanocages, the title MOF exhibited promising potential for the multifunctional separation of C2H2/C2H4 and C2H2/CO2/CH4 mixtures under ambient conditions, as shown by pure-composition isotherm measurements, IAST predictions, and molecular modeling studies.

Switch Control Inhibition of KIT and PDGFRA in Patients With Advanced Gastrointestinal Stromal Tumor: A Phase I Study of Ripretinib.

PURPOSE: In advanced gastrointestinal stromal tumor (GIST), there is an unmet need for therapies that target both primary and secondary mutations of pathogenic KIT/PDGFRA oncoproteins. Ripretinib is a novel switch-control kinase inhibitor designed to inhibit a wide range of KIT and PDGFRA mutations. PATIENTS AND METHODS: This first-in-human, to our knowledge, phase I study of ripretinib (ClinicalTrials.gov identifier: NCT02571036) included a dose-escalation phase and subsequent expansion phase at the recommended phase II dose (RP2D). Eligible patients included those with advanced GIST, intolerant to or experienced progression on ≥ 1 line of systemic therapy, and other advanced malignancies. Safety, dose-limiting toxicities (DLTs), maximum-tolerated dose (MTD), and preliminary antitumor activity were evaluated. RESULTS: At data cutoff (August 31, 2019), 258 patients (n = 184 GIST) were enrolled, with 68 patients in the dose-escalation phase. Three DLTs were reported: grade 3 lipase increase (n = 2; 100 mg and 200 mg twice a day) and grade 4 increased creatine phosphokinase (n = 1; 150 mg once daily). MTD was not reached (maximum dose evaluated, 200 mg twice a day); 150 mg once daily was established as the RP2D. The most frequent (> 30%) treatment-emergent adverse events in patients with GIST receiving ripretinib 150 mg once daily (n = 142) were alopecia (n = 88 [62.0%]), fatigue (n = 78 [54.9%]), myalgia (n = 69 [48.6%]), nausea (n = 65 [45.8%]), palmar-plantar erythrodysesthesia (n = 62 [43.7%]), constipation (n = 56 [39.4%]), decreased appetite (n = 48 [33.8%]), and diarrhea (n = 47 [33.1%]). Objective response rate (confirmed) of 11.3% (n = 16/142) ranging from 7.2% (n = 6/83; fourth line or greater) to 19.4% (n = 6/31; second line) and median progression-free survival ranging from 5.5 months (fourth line or greater) to 10.7 months (second line), on the basis of investigator assessment, were observed. CONCLUSION: Ripretinib is a well-tolerated, novel inhibitor of KIT and PDGFRA mutant kinases with promising activity in patients with refractory advanced GIST.

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa.

The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved large-scale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

Stimulatory Effects of Boscalid on Virulence of Sclerotinia sclerotiorum Indicate Hormesis May Be Masked by Inhibitions.

Hormetic effects of fungicides on phytopathogens are of great importance for proper application of fungicides. The aim of the present study was to investigate the stimulatory effects of the fungicide boscalid on mycelial growth and virulence of the devastating plant pathogen Sclerotinia sclerotiorum. Boscalid in potato dextrose agar (PDA) at a dosage range from 0.0005 to 0.002 µg/ml exerted statistically significant (P ≤ 0.015) stimulations on mycelial growth of S. sclerotiorum, and the maximum stimulation magnitudes were 5.55 ± 0.73% (mean ± SD) for the four isolates tested. Boscalid in PDA at 0.02 µg/ml inhibited mycelial growth of isolates HLJ3H and HLJ4H by 15.0 and 8.9%, respectively. However, after the growth-inhibited mycelia were inoculated on rapeseed leaves, isolates HLJ3H and HLJ4H exhibited virulence stimulations of 8.7 and 17.8%, respectively, indicating that hormesis may be masked by inhibitions. Boscalid sprayed at 0.0001 to 0.1 µg/ml on detached rapeseed leaves had significant (P ≤ 0.041) stimulations on virulence of S. sclerotiorum, and the maximum stimulation magnitudes were 17.90 ± 5.94% (mean ± SD) for the four isolates tested. Experiments on 12 isolates with different levels of virulence showed there was a negative correlation (R = -0.663, P = 0.019) between the maximum virulence stimulation magnitude and virulence of S. sclerotiorum in the absence of fungicide. Boscalid at stimulatory concentrations had no significant effect on the expression levels of three virulence-associated genes that encode cutinase (SsCut), polygalacturonase (SsPG1), and oxaloacetate acetylhydrolase (SsOah1). The molecular mechanisms for hormetic effects of boscalid on S. sclerotiorum remain to be studied in the future.

Safety and Efficacy of Teduglutide in Pediatric Patients With Intestinal Failure due to Short Bowel Syndrome: A 24-Week, Phase III Study.

BACKGROUND: This study evaluated the safety and efficacy of teduglutide in pediatric patients with short bowel syndrome-associated intestinal failure (SBS-IF). METHODS: A 24-week, phase III trial with 2 randomized, double-blind teduglutide dose groups and a nonblinded standard of care (SOC) arm was used; patients received 0.025 mg/kg or 0.05 mg/kg teduglutide once daily. Safety end points included treatment-emergent adverse events (TEAEs) and growth parameters. The primary efficacy/pharmacodynamic end point was the number of patients who achieved a ≥20% reduction in parenteral support (PS) from baseline at week 24. RESULTS: All 59 enrolled patients completed the study (0.025 mg/kg, n = 24; 0.05 mg/kg, n = 26; SOC, n = 9). Baseline demographics and disease characteristics were comparable among groups. TEAEs were reported by 98% and 100% of patients in the teduglutide and SOC groups, respectively. The most common TEAEs in the teduglutide-treated groups were pyrexia and vomiting. The primary end point was achieved by 13 (54.2%), 18 (69.2%), and 1 (11.1%) patients who received 0.025 mg/kg teduglutide, 0.05 mg/kg teduglutide, and SOC, respectively (P < 0.05 vs SOC). Both 0.025-mg/kg and 0.05-mg/kg teduglutide groups showed clinically significant reductions in PS volume (P < 0.05 vs SOC), PS calories, days per week and hours per day of PS infusions, and increases in enteral nutrition and plasma citrulline at week 24 compared with baseline. Two (8.3%, 0.025 mg/kg teduglutide) and 3 patients (11.5%, 0.05 mg/kg teduglutide) achieved enteral autonomy. CONCLUSION: The safety profile of teduglutide was similar to that reported previously in children and adults. Treatment with teduglutide was associated with significant reductions in PS for pediatric patients with SBS-IF over 24 weeks.

Establishment and optimization of mRNA in situ hybridization system in turnip (Brassica rapa var. rapa).

BACKGROUND: In situ hybridization (ISH) is a general molecular biological technique used to determine the spatiotemporal expression of genes in many species. In the past few years, numerous ISH protocols have been established in many species. Turnip (Brassica rapa var. rapa) is an important crop in the world, especially in the Plateau area of China, and is a traditional Tibetan medicine. However, ISH protocol in turnip has not been established. RESULTS: We explored and established an optimal workflow for mRNA ISH system for turnip which has been evaluated using BrrCLV3 and BrrWUSa. The optimal methods include: (1) fixation method, (2) protease K pretreatment time, (3) probe length and concentration, (4) washing temperature. We also provide advice on weakening background and improving the efficiency of RNA transcription in vitro. The expression of the BrrCLV3 gene in turnip was detected by the optimized system, and the applicability of the system was confirmed by using BrrWUSa. CONCLUSIONS: In this study, we established and optimized the mRNA ISH system for turnip. We explored and found that (1) FAA fixative was the optimized fixation method, (2) 30 min was the optimized protease K pretreatment time, (3) 100 bp, 100 ng/ml probe had good hybridization signal, (4) the optimized washing temperature was 52 °C. It provides a powerful method to locate mRNA in the tissue, which can study the expression and function of turnip's genes. As such, it has considerable advantages in terms of time and cost.

Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed.

The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29 °C, 33 °C, and 35 °C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29 °C to a metazoan-dominated diet at 35 °C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29 °C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33 °C, as evaluated by the Ivlev's selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.

Unexpected prey of juvenile spotted scat (Scatophagus argus) near a wharf: The prevalence of fouling organisms in stomach contents.

A knowledge of fish diets can contribute to revealing the trophic role and ecological function of species in aquatic ecosystems. At present, however, there are no efficient or comprehensive methods for analyzing fish diets. In this study, we investigated the diets of juvenile Scatophagus argus collected near a wharf in Daya Bay, China, by dissection and high-throughput sequencing (HTS) using the 18S rDNA V4 region. Microscopy disclosed large amounts of bryozoans and unrecognizable detritus. In contrast, HTS analysis indicated that the fish diets were considerably more diverse than visual inspection suggested. After eliminating fish sequences, approximately 17,000 sequences from taxa in nine phyla (Ciliophora, Bryozoa, Annelida, Bacillariophyta, Chlorophyta, Arthropoda, Dinoflagellata, Tunicata, and Phaeophyta) were identified from the analysis of stomach contents. Twenty-one food categories were identified, most of which (95.2%) were benthic fouling organisms that could easily be collected around wharfs. These consisted of bryozoans (31.9%), ciliates (45.7%), polychaetes (14.6%), and green algae (3.0%). Therefore, to adapt to anthropogenic habitat modification, the fish had probably shifted from planktonic to benthic feeding. The prevalence of fouling organisms in the stomachs of juvenile S. argus indicates that the fish have responded to habitat changes by widening their food spectrum. This adaptation may have increased their chances of survival. The fouling organisms that inhabit highly perturbed coastal ecosystems could represent a food source for animals at higher trophic levels. Our results accordingly suggest that human activity might significantly influence fish feeding behavior and material transfer along the food chain.

Genome-Wide Identification and Characterization of BrrTCP Transcription Factors in Brassica rapa ssp. rapa.

The teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family is a plant-specific transcription factor that participates in the control of plant development by regulating cell proliferation. However, no report is currently available about this gene family in turnips (Brassica rapa ssp. rapa). In this study, a genome-wide analysis of TCP genes was performed in turnips. Thirty-nine TCP genes in turnip genome were identified and distributed on 10 chromosomes. Phylogenetic analysis clearly showed that the family was classified as two clades: class I and class II. Gene structure and conserved motif analysis showed that the same clade genes have similar gene structures and conserved motifs. The expression profiles of 39 TCP genes were determined through quantitative real-time PCR. Most CIN-type BrrTCP genes were highly expressed in leaf. The members of CYC/TB1 subclade are highly expressed in flower bud and weakly expressed in root. By contrast, class I clade showed more widespread but less tissue-specific expression patterns. Yeast two-hybrid data show that BrrTCP proteins preferentially formed heterodimers. The function of BrrTCP2 was confirmed through ectopic expression of BrrTCP2 in wild-type and loss-of-function ortholog mutant of Arabidopsis. Overexpression of BrrTCP2 in wild-type Arabidopsis resulted in the diminished leaf size. Overexpression of BrrTCP2 in triple mutants of tcp2/4/10 restored the leaf phenotype of tcp2/4/10 to the phenotype of wild type. The comprehensive analysis of turnip TCP gene family provided the foundation to further study the roles of TCP genes in turnips.

Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.

Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of copepods.

Ponatinib in refractory Philadelphia chromosome-positive leukemias.

BACKGROUND: Resistance to tyrosine kinase inhibitors in patients with chronic myeloid leukemia (CML) and Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph-positive ALL) is frequently caused by mutations in the BCR-ABL kinase domain. Ponatinib (AP24534) is a potent oral tyrosine kinase inhibitor that blocks native and mutated BCR-ABL, including the gatekeeper mutant T315I, which is uniformly resistant to tyrosine kinase inhibitors. METHODS: In this phase 1 dose-escalation study, we enrolled 81 patients with resistant hematologic cancers, including 60 with CML and 5 with Ph-positive ALL. Ponatinib was administered once daily at doses ranging from 2 to 60 mg. Median follow-up was 56 weeks (range, 2 to 140). RESULTS: Dose-limiting toxic effects included elevated lipase or amylase levels and pancreatitis. Common adverse events were rash, myelosuppression, and constitutional symptoms. Among Ph-positive patients, 91% had received two or more approved tyrosine kinase inhibitors, and 51% had received all three approved tyrosine kinase inhibitors. Of 43 patients with chronic-phase CML, 98% had a complete hematologic response, 72% had a major cytogenetic response, and 44% had a major molecular response. Of 12 patients who had chronic-phase CML with the T315I mutation, 100% had a complete hematologic response and 92% had a major cytogenetic response. Of 13 patients with chronic-phase CML without detectable mutations, 100% had a complete hematologic response and 62% had a major cytogenetic response. Responses among patients with chronic-phase CML were durable. Of 22 patients with accelerated-phase or blast-phase CML or Ph-positive ALL, 36% had a major hematologic response and 32% had a major cytogenetic response. CONCLUSIONS: Ponatinib was highly active in heavily pretreated patients with Ph-positive leukemias with resistance to tyrosine kinase inhibitors, including patients with the BCR-ABL T315I mutation, other mutations, or no mutations. (Funded by Ariad Pharmaceuticals and others; ClinicalTrials.gov number, NCT00660920.).

Prevalent ciliate symbiosis on copepods: high genetic diversity and wide distribution detected using small subunit ribosomal RNA gene.

Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA)-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups), six (containing 99% of all the sequences) belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus), and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally.

Phase I study of pemetrexed and pegylated liposomal doxorubicin in patients with refractory breast, ovarian, primary peritoneal, or fallopian tube cancer.

PURPOSE: Pemetrexed and pegylated liposomal doxorubicin (PLD) are clinically active as single agents and preclinically synergistic. This phase I, open-label trial evaluated the maximum tolerated dose (MTD) and safety of pemetrexed followed by PLD in patients with breast or gynecologic cancers. PATIENTS: Using 3 + 3 dose escalation, cohorts of 3-9 patients received escalating doses of pemetrexed 400-500 mg/m(2) on days 1 and 15 and PLD 30-45 mg/m(2) on day 1 of a 28-day cycle. All patients received folic acid and vitamin B(12) until 21 days after last pemetrexed dose. Patients continued until dose-limiting toxicity (DLT) or progression (PD). RESULTS: From 11/05 to 2/08, 29 patients entered treatment; median age: 60.6 years (range, 47.5-80.1); ECOG PS 0/1: 27.6%/72.4%; primary disease site: ovarian (55.2%), breast (34.5%), peritoneum (10.3%); prior therapies: chemotherapy (100.0%), surgery (72.4%), hormones/biologics (35%), and radiation (20.7%). Pemetrexed/PLD dose levels: L1 = 400/30 (n = 4), L2 = 400/35 (n = 6), L3 = 500/35 (n = 9), L4 = 500/40 (n = 7), and L5 = 500/45 (n = 3). Treatment-related grade 3-4 toxicities: hematologic-neutropenia (86.2%), leukopenia (58.6%), thrombocytopenia (48.3%), anemia (41.4%); nonhematologic-mucosal inflammation (24.1%), febrile neutropenia (24.1%), hand-foot syndrome (13.8%), hypokalaemia (10.3%). Reasons for discontinuation: PD (48.3%), toxicity (27.6%), patient request (13.8%), and investigator request (10.3%). EFFICACY: 5 ovarian patients (20.8%) achieved partial response; median time to progression (TTP) was 6.1 months (range, 1.2-12.5). CONCLUSION: Pemetrexed plus PLD was reasonably tolerated in this heavily-pretreated population. MTD: pemetrexed 500 mg/m(2) and PLD 40 mg/m(2) may be carried forward to phase II studies in specific patient populations. TTP in platinum-refractory ovarian patients was greater than expected.

Statistical redundancy testing for improved gene selection in cancer classification using microarray data.

In gene selection for cancer classification using microarray data, we define an eigenvalue-ratio statistic to measure a gene's contribution to the joint discriminability when this gene is included into a set of genes. Based on this eigenvalue-ratio statistic, we define a novel hypothesis testing for gene statistical redundancy and propose two gene selection methods. Simulation studies illustrate the agreement between statistical redundancy testing and gene selection methods. Real data examples show the proposed gene selection methods can select a compact gene subset which can not only be used to build high quality cancer classifiers but also show biological relevance.