de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project

Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research (SPARK), and the 1000 Genomes Project (1000G) that were sequenced using DNA from blood, saliva, and lymphoblastoid cell lines (LCLs), respectively. The SSC and SPARK DNV callsets were within expectations for number of DNVs, percent at CpG sites, phasing to the paternal chromosome of origin, and average allele balance. However, the 1000G DNV callset was not within expectations and contained excessive DNVs that are likely cell line artifacts. Mutation signature analysis revealed 30% of 1000G DNV signatures matched B-cell lymphoma. Furthermore, we found variants in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites and significant excess of protein-coding DNVs in IGLL5; a gene known to be involved in B-cell lymphomas. Our study provides a new rapid DNV caller for the field and elucidates important implications of using sequencing data from LCLs for reference building and disease-related projects.

Autonomous robotic laparoscopic surgery for intestinal anastomosis

Autonomous robotic surgery has the potential to provide efficacy, safety, and consistency independent of individual surgeon's skill and experience. Autonomous anastomosis is a challenging soft-tissue surgery task because it requires intricate imaging, tissue tracking, and surgical planning techniques, as well as a precise execution via highly adaptable control strategies often in unstructured and deformable environments. In the laparoscopic setting, such surgeries are even more challenging because of the need for high maneuverability and repeatability under motion and vision constraints. Here we describe an enhanced autonomous strategy for laparoscopic soft tissue surgery and demonstrate robotic laparoscopic small bowel anastomosis in phantom and in vivo intestinal tissues. This enhanced autonomous strategy allows the operator to select among autonomously generated surgical plans and the robot executes a wide range of tasks independently. We then use our enhanced autonomous strategy to perform in vivo autonomous robotic laparoscopic surgery for intestinal anastomosis on porcine models over a 1-week survival period. We compared the anastomosis quality criteria-including needle placement corrections, suture spacing, suture bite size, completion time, lumen patency, and leak pressure-of the developed autonomous system, manual laparoscopic surgery, and robot-assisted surgery (RAS). Data from a phantom model indicate that our system outperforms expert surgeons' manual technique and RAS technique in terms of consistency and accuracy. This was also replicated in the in vivo model. These results demonstrate that surgical robots exhibiting high levels of autonomy have the potential to improve consistency, patient outcomes, and access to a standard surgical technique.

Supervised Autonomous Electrosurgery via Biocompatible Near-Infrared Tissue Tracking Techniques

Autonomous robotic surgery systems aim to improve patient outcomes by leveraging the repeatability and consistency of automation and also reducing human induced errors. However, intraoperative autonomous soft tissue tracking and robot control still remains a challenge due to the lack of structure, and high deformability of such tissues. In this paper, we take advantage of biocompatible Near-Infrared (NIR) marking methods and develop a supervised autonomous 3D path planning, filtering, and control strategy for our Smart Tissue Autonomous Robot (STAR) to enable precise and consistent incisions on complex 3D soft tissues. Our experimental results on cadaver porcine tongue samples indicate that the proposed strategy reduces surface incision error and depth incision error by 40.03% and 51.5%, respectively, compared to a teleoperation strategy via da Vinci. Furthermore, compared to an autonomous path planning method with linear interpolation between the NIR markers, the proposed strategy reduces the incision depth error by 48.58% by taking advantage of 3D tissue surface information.

Semi-autonomous Robotic Anastomoses of Vaginal Cuffs Using Marker Enhanced 3D Imaging and Path Planning

Autonomous robotic anastomosis has the potential to improve surgical outcomes by performing more consistent suture spacing and bite size compared to manual anastomosis. However, due to soft tissue's irregular shape and unpredictable deformation, performing autonomous robotic anastomosis without continuous tissue detection and three-dimensional path planning strategies remains a challenging task. In this paper, we present a novel three-dimensional path planning algorithm for Smart Tissue Autonomous Robot (STAR) to enable semi-autonomous robotic anastomosis on deformable tissue. The algorithm incorporates (i) continuous detection of 3D near infrared (NIR) markers manually placed on deformable tissue before the procedure, (ii) generating a uniform and consistent suture placement plan using 3D path planning methods based on the locations of the NIR markers, and (iii) updating the remaining suture plan after each completed stitch using a non-rigid registration technique to account for tissue deformation during anastomosis. We evaluate the path planning algorithm for accuracy and consistency by comparing the anastomosis of synthetic vaginal cuff tissue completed by STAR and a surgeon. Our test results indicate that STAR using the proposed method achieves 2.6 times better consistency in suture spacing and 2.4 times better consistency in suture bite sizes than the manual anastomosis.

B-54 Insights into a Novel Integrated Screening Clinic: Parent Perceptions of Emotional Functioning in Acute Recovery Phase Following Pediatric Neurocritical Care

Objective

Children with traumatic brain injury (TBI) requiring neurocritical care are at high risk for neurocognitive, emotional, physical, and psychosocial difficulties, collectively known as Post-Intensive Care Syndrome. Our study sought to characterize parent ratings of emotional functioning in the acute recovery phase based upon mechanism of injury.

Method

Twenty children (Mdn = 12.6 years, IQR = 9-15; 65% male) were screened as part of a multidisciplinary follow-up clinic 1-month following hospital discharge. Emotional functioning was assessed using PROMIS Parent Proxy Report for Anxiety and Depression. A brief neurocognitive battery estimated presence of cognitive impairment. MANCOVA was used to compare emotional functioning across injury mechanism (high velocity injury [HVI], 65%; fall, 35%).

Results

Groups did not differ on age, gender, and presence of cognitive impairment. After controlling for severity, mechanism of injury had a significant effect on both anxiety (p = .026) and depression (p = .004). The HVI group had mildly elevated anxiety (M = 50.5, SD = 12.2) and depression (M = 54.2, SD = 10.6) scores, while the fall group had anxiety (M = 38.0, SD = 6.2) and depression (M = 39.0, SD = 7.3) scores within normal limits.

Conclusions

In the acute recovery phase following TBI, anxiety and depression symptoms are more common after HVI than falls, even when controlling for severity of injury. The HVI group includes injuries resulting from motor vehicle accidents which may have a broader impact on the family and may explain higher rates of emotional distress in this patient group compared to other mechanisms of TBI. Additional research is needed to further explore variables related to emotional functioning following TBI and how they change over the course of recovery.

Autonomous Laparoscopic Robotic Suturing with a Novel Actuated Suturing Tool and 3D Endoscope

Compared to open surgical techniques, laparoscopic surgical methods aim to reduce the collateral tissue damage and hence decrease the patient recovery time. However, constraints imposed by the laparoscopic surgery, i.e. the operation of surgical tools in limited spaces, turn simple surgical tasks such as suturing into time-consuming and inconsistent tasks for surgeons. In this paper, we develop an autonomous laparoscopic robotic suturing system. More specific, we expand our smart tissue anastomosis robot (STAR) by developing i) a new 3D imaging endoscope, ii) a novel actuated laparoscopic suturing tool, and iii) a suture planning strategy for the autonomous suturing. We experimentally test the accuracy and consistency of our developed system and compare it to sutures performed manually by surgeons. Our test results on suture pads indicate that STAR can reach 2.9 times better consistency in suture spacing compared to manual method and also eliminate suture repositioning and adjustments. Moreover, the consistency of suture bite sizes obtained by STAR matches with those obtained by manual suturing.

A Confidence-Based Shared Control Strategy for the Smart Tissue Autonomous Robot (STAR)

Autonomous robotic assisted surgery (RAS) systems aim to reduce human errors and improve patient outcomes leveraging robotic accuracy and repeatability during surgical procedures. However, full automation of RAS in complex surgical environments is still not feasible and collaboration with the surgeon is required for safe and effective use. In this work, we utilize our Smart Tissue Autonomous Robot (STAR) to develop and evaluate a shared control strategy for the collaboration of the robot with a human operator in surgical scenarios. We consider 2D pattern cutting tasks with partial blood occlusion of the cutting pattern using a robotic electrocautery tool. For this surgical task and RAS system, we i) develop a confidence-based shared control strategy, ii) assess the pattern tracking performances of manual and autonomous controls and identify the confidence models for human and robot as well as a confidence-based control allocation function, and iii) experimentally evaluate the accuracy of our proposed shared control strategy. In our experiments on porcine fat samples, by combining the best elements of autonomous robot controller with complementary skills of a human operator, our proposed control strategy improved the cutting accuracy by 6.4%, while reducing the operator work time to 44 % compared to a pure manual control.

Abstract P3-06-05: Receptor-mediated binding of HER2-targeted antibody-liposomal doxorubicin conjugate MM-302 increases liposome binding, nuclear doxorubicin, DNA damage and efficacy relative to untargeted PEGylated liposomal doxorubicin (PLD/Doxil)

This abstract was withdrawn by the authors.

The value of uncertainty in critical illness? An ethnographic study of patterns and conflicts in care and decision-making trajectories

BACKGROUND

With increasingly intensive treatments and population ageing, more people face complex treatment and care decisions. We explored patterns of the decision-making processes during critical care, and sources of conflict and resolution.

METHODS

Ethnographic study in two Intensive Care Units (ICUs) in an inner city hospital comprising: non-participant observation of general care and decisions, followed by case studies where treatment limitation decisions, comfort care and/or end of life discussions were occurring. These involved: semi-structured interviews with consenting families, where possible, patients; direct observations of care; and review of medical records.

RESULTS

Initial non-participant observation included daytime, evenings, nights and weekends. The cases were 16 patients with varied diagnoses, aged 19-87 years; 19 family members were interviewed, aged 30-73 years. Cases were observed for <1 to 156 days (median 22), depending on length of ICU admission. Decisions were made serially over the whole trajectory, usually several days or weeks. We identified four trajectories with distinct patterns: curative care from admission; oscillating curative and comfort care; shift to comfort care; comfort care from admission. Some families considered decision-making a negative concept and preferred uncertainty. Conflict occurred most commonly in the trajectories with oscillating curative and comfort care. Conflict also occurred inside clinical teams. Families were most often involved in decision-making regarding care outcomes and seemed to find it easier when patients switched definitively from curative to comfort care. We found eight categories of decision-making; three related to the care outcomes (aim, place, response to needs) and five to the care processes (resuscitation, decision support, medications/fluids, monitoring/interventions, other specialty involvement).

CONCLUSIONS

Decision-making in critical illness involves a web of discussions regarding the potential outcomes and processes of care, across the whole disease trajectory. When measures oscillate between curative and comfort there is greatest conflict. This suggests a need to support early communication, especially around values and preferred care outcomes, from which other decisions follow, including DNAR. Offering further support, possibly with expert palliative care, communication, and discussion of 'trial of treatment' may be beneficial at this time, rather than waiting until the 'end of life'.

Endoscopic-CT: Learning-Based Photometric Reconstruction for Endoscopic Sinus Surgery

In this work we present a method for dense reconstruction of anatomical structures using white light endoscopic imagery based on a learning process that estimates a mapping between light reflectance and surface geometry. Our method is unique in that few unrealistic assumptions are considered (i.e., we do not assume a Lambertian reflectance model nor do we assume a point light source) and we learn a model on a per-patient basis, thus increasing the accuracy and extensibility to different endoscopic sequences. The proposed method assumes accurate video-CT registration through a combination of Structure-from-Motion (SfM) and Trimmed-ICP, and then uses the registered 3D structure and motion to generate training data with which to learn a multivariate regression of observed pixel values to known 3D surface geometry. We demonstrate with a non-linear regression technique using a neural network towards estimating depth images and surface normal maps, resulting in high-resolution spatial 3D reconstructions to an average error of 0.53mm (on the low side, when anatomy matches the CT precisely) to 1.12mm (on the high side, when the presence of liquids causes scene geometry that is not present in the CT for evaluation). Our results are exhibited on patient data and validated with associated CT scans. In total, we processed 206 total endoscopic images from patient data, where each image yields approximately 1 million reconstructed 3D points per image.

Rendering-Based Video-CT Registration with Physical Constraints for Image-Guided Endoscopic Sinus Surgery

We present a system for registering the coordinate frame of an endoscope to pre- or intra- operatively acquired CT data based on optimizing the similarity metric between an endoscopic image and an image predicted via rendering of CT. Our method is robust and semi-automatic because it takes account of physical constraints, specifically, collisions between the endoscope and the anatomy, to initialize and constrain the search. The proposed optimization method is based on a stochastic optimization algorithm that evaluates a large number of similarity metric functions in parallel on a graphics processing unit. Images from a cadaver and a patient were used for evaluation. The registration error was 0.83 mm and 1.97 mm for cadaver and patient images respectively. The average registration time for 60 trials was 4.4 seconds. The patient study demonstrated robustness of the proposed algorithm against a moderate anatomical deformation.

Preeclamptic cord blood hemolysis and the effect of Monascus purpureus and Saccharomyces cerevisiae in modulating preeclamptic stress

BACKGROUND

Preeclampsia is associated with impaired antioxidant defense that results in materno- fetal complications. In addition to antioxidant deficiency, hemolytic disorder has also been observed in preeclamptic mother.

METHODS

This study aims in analyzing the fetal complications using cord blood RBC (red blood cell); further the antihemolytic and antioxidant efficiency of two common probiotic yeasts Monascus purpureus and Saccharomyces cerevisiae in preeclamptic and normotensive RBCs were assessed.

RESULTS

There was a significant decrease in the antioxidant status (p<0.05) with increased oxidative stress, nitrative stress (p<0.05) and hemolysis (p<0.001) in preeclamptic RBC comparatively. M. purpureus demonstrated a highly significant reactive oxygen radical scavenging activity (p<0.001) whereas S. cerevisiae exhibited a highly significant nitric oxide radical scavenging activity (p<0.001). It was noted that oxidative stress hemolysis was decreased with increased antioxidant level in cord blood RBC from both samples after incubation with both yeasts in a similar manner. The antihemolytic property of M. purpureus and S. cerevisiae suggests that S. cerevisiae functions efficiently with increasing stress.

CONCLUSION

This study demonstrates for the first time that despite their differential scavenging activities, a diet rich in M. purpureus and S. cerevisiae could equally serve as a good natural supplement to alleviate the stress status in the preeclamptic fetus (Tab. 4, Fig. 1, Ref. 39).

Complications of nasogastric tube placement--don't blow it

Preventable complications maybe associated with the placement of nasogastric tubes. Our report raises awareness of the potentially fatal complications that can occur. We also recommend an approach for clinicians which maybe used to avoid significant patient morbidity.

Prenatal stress differentially alters brain-derived neurotrophic factor expression and signaling across rat strains

BACKGROUND

Psychiatric illness and anxiety disorders have strong neurodevelopmental components. Environmental insults such as prenatal exposure to stress and genetic differences in stress responses may affect brain development.

METHODS

A rat model of random variable prenatal stress was used to study the expression and processing of hippocampal brain-derived neurotrophic factor (BDNF) in the offspring of the stressed rat dams. To account for unknown genetic influences that may play a role in the outcome of this prenatal stress paradigm, three different rat strains with known differences in stress responsivity were studied: Fischer, Sprague-Dawley, and Lewis rats (n=132).

RESULTS

Multiple disparities in mRNA expression levels of BDNF, and transcripts related to its processing and signaling were found in the three strains. Of the numerous splice variants transcribed from the BDNF gene, the transcript containing BDNF exon VI was most aberrant in the prenatally stressed animals. Protein levels of both uncleaved proBDNF and mature BDNF were also altered, as was intra-cellular signaling by phosphorylation of the neurotrophic tyrosine kinase receptor type 2 (NTRK2, TrkB) and mitogen-activated protein kinase (Erk 1/2). Changes were not only dependent on prenatal stress, but were also strain dependent, demonstrating the importance of genetic background.

CONCLUSION

BDNF signaling provides both positive neurotrophic support for neurons and negative apoptotic effects, both of which may contribute to behavioral or neurochemical outcomes after prenatal exposure to stress. Differential processing of BDNF after prenatal stress in the three rat strains has implications for human subjects where genetic differences may protect or exacerbate the effects of an environmental stressor during fetal development.

Genotoxicity of carbon nanofibers: are they potentially more or less dangerous than carbon nanotubes or asbestos?

The production of carbon nanofibers and nanotubes (CNF/CNT) and their composite products is increasing globally. CNF are generating great interest in industrial sectors such as energy production and electronics, where alternative materials may have limited performance or are produced at a much higher cost. However, despite the increasing industrial use of carbon nanofibers, information on their potential adverse health effects is limited. In the current study, we examine the cytotoxic and genotoxic potential of carbon-based nanofibers (Pyrograf®-III) and compare this material with the effects of asbestos fibers (crocidolite) or single-walled carbon nanotubes (SWCNT). The genotoxic effects in the lung fibroblast (V79) cell line were examined using two complementary assays: the comet assay and micronucleus (MN) test. In addition, we utilized fluorescence in situ hybridization to detect the chromatin pan-centromeric signals within the MN indicating their origin by aneugenic (chromosomal malsegregation) or clastogenic (chromosome breakage) mechanisms. Cytotoxicity tests revealed a concentration- and time-dependent loss of V79 cell viability after exposure to all tested materials in the following sequence: asbestos>CNF>SWCNT. Additionally, cellular uptake and generation of oxygen radicals was seen in the murine RAW264.7 macrophages following exposure to CNF or asbestos but not after administration of SWCNT. DNA damage and MN induction were found after exposure to all tested materials with the strongest effect seen for CNF. Finally, we demonstrated that CNF induced predominantly centromere-positive MN in primary human small airway epithelial cells (SAEC) indicating aneugenic events. Further investigations are warranted to elucidate the possible mechanisms involved in CNF-induced genotoxicity.

A heavy heart; A massive right atrial myxoma causing fatigue and shortness of breath

Cardiac myxomas are rare. The clinical diagnosis of an atrial myxoma may occur in an asymptomatic patient but may also present with cardiac failure, syncope, arrythmias, or with vascular evidence of tumour embolisation. The delay in diagnosis from presentation is approximately ten months. We present the case of a 53-year-old woman who attended our Emergency Department with dyspnoea, fatigue and left sided chest pain. Investigations revealed a massive right atrial myxoma. The tumour was resected successfully. Emergency Physicians should be aware of the subtle ways in which an atrial myxoma can present because of the potential for fatal outcomes.

Size-dependent effects of tungsten carbide-cobalt particles on oxygen radical production and activation of cell signaling pathways in murine epidermal cells

Hard metal or cemented carbide consists of a mixture of tungsten carbide (WC) (85%) and metallic cobalt (Co) (5-15%). WC-Co is considered to be potentially carcinogenic to humans. However, no comparison of the adverse effects of nano-sized WC-Co particles is available to date. In the present study, we compared the ability of nano- and fine-sized WC-Co particles to form free radicals and propensity to activate the transcription factors, AP-1 and NF-kappaB, along with stimulation of mitogen-activated protein kinase (MAPK) signaling pathways in a mouse epidermal cell line (JB6 P(+)). Our results demonstrated that nano-WC-Co generated a higher level of hydroxyl radicals, induced greater oxidative stress, as evidenced by a decrease of GSH levels, and caused faster JB6 P(+) cell growth/proliferation than observed after exposure of cells to fine WC-Co. In addition, nano-WC-Co activated AP-1 and NF-kappaB more efficiently in JB6(+/+) cells as compared to fine WC-Co. Experiments using AP-1-luciferase reporter transgenic mice confirmed the activation of AP-1 by nano-WC-Co. Nano- and fine-sized WC-Co particles also stimulated MAPKs, including ERKs, p38, and JNKs with significantly higher potency of nano-WC-Co. Finally, co-incubation of the JB6(+/+) cells with N-acetyl-cysteine decreased AP-1 activation and phosphorylation of ERKs, p38 kinase, and JNKs, thus suggesting that oxidative stress is involved in WC-Co-induced toxicity and AP-1 activation.

Magnitude of progression-free survival (PFS) improvement and treatment (Tx) duration in metastatic colorectal cancer (mCRC) for bevacizumab (BV) in combination with oxaliplatin-containing regimens: An analysis of two phase III studies

4073

Background: In trials of BV with FOLFOX (fluorouracil, leucovorin, oxaliplatin) for mCRC, variability in the magnitude of PFS improvement has been reported [HR=0.61 in E3200 vs HR= 0.83 (FOLFOX or CAPOX (capecitabine and oxaliplatin)) in NO16966]. We propose that differences in rates of treatment discontinuation (D/C) for adverse events (AE) between these studies may have resulted in differences in the observed benefits associated with BV. We explored Tx duration (proportion of patients on Tx) and Tx D/C data at median PFS for the BV containing arms of each study. Methods: ECOG study E3200 randomized previously treated patients with mCRC to FOLFOX ± BV (10 mg/kg). NO16966 employed a 2x2 design that randomized previously untreated patients with mCRC to CAPOX vs FOLFOX and to BV (5 mg/kg) or placebo. In both trials, study Tx was defined as any component of the prescribed regimen. PFS was estimated from Kaplan-Meier curves, and hazard ratios (HR) for PFS were estimated by Cox regression. Results: Median PFS for the BV containing arm of the study: 30 weeks for E3200; 42 weeks for NO16966 Conclusion: These data suggest possible differences between the two studies in Tx duration and Tx D/C patterns with a greater proportion of patients on NO16966 discontinuing Tx for any AE. Duration of study Tx might have affected both the incidence of AEs and the magnitude of PFS benefit observed for the addition of bevacizumab to oxaliplatin-based chemotherapy in these studies. Attention to Tx duration and Non-PD Tx D/C in future clinical trials will be important when considering PFS as a primary efficacy endpoint.

[Table: see text]

No significant financial relationships to disclose.

Brain pH has a significant impact on human postmortem hippocampal gene expression profiles

Studies of neurobiological disorders in the brain, including schizophrenia, rely on the use of postmortem brain tissues, in which an understanding of the effects of various pre- and postmortem variables on gene expression is critical. In several different brain regions, pH has been shown to have a large effect on postmortem brain gene expression patterns. One region that has not yet been evaluated in such studies is the hippocampus, a region often implicated in schizophrenia research. In the present study, we show that postmortem brain pH is similar across different brain regions. Brain pH accounted for greater variation in hippocampal gene expression profiles than any other parameter evaluated, including gender and schizophrenia. The predictive value of brain pH in an independent sample set was also greater than the disease, demonstrating that pH represents one of the most important control parameters in human postmortem gene expression studies in schizophrenia.

Mechanisms regulating immune cell contributions to spiral artery modification -- facts and hypotheses -- a review

Early during murine, human and porcine pregnancy, endometrium associated with developing placentae is enriched for uterine Natural Killer (uNK) cells. A shared role for uNK cells in each of these species is production of angiogenic growth factors. Many uNK cells are located in close proximity to or structurally integrated within the walls of endometrial vessels. In mice, uNK cells have been found essential for the initiation of pregnancy-associated spiral arterial modification through their production of interferon-gamma. Unique aspects of uNK cell interactions with decidual endothelium are being defined using cell and tissue transfer into pregnant, alymphoid mice, adhesion of viable lymphocytes to frozen uterine tissue sections under shear forces, laser capture microdissection of uNK cells for quantitative RNA analyses and intravital microscopy. These studies indicate that uterine lymphocytes have a fundamental and major importance in promotion of angiogenesis within implantation sites that is regulated by the reproductive hormone cycle. Further, this work suggests that the pro-inflammatory endometrial cytokine response seen when peri-implantation conceptuses arrest has, as its target for destruction, newly developed endometrial vasculature rather than fetal trophoblast.

Characterization of allelic variants at chromosome 15q14 in schizophrenia

Evidence of genetic linkage for schizophrenia at chromosome 15q14 has been reported in nine independent studies, but the molecular variants responsible for transmission of genetic risk are unknown. National Institute of Mental Health Schizophrenia Genetics Initiative families were genotyped for single nucleotide polymorphisms (SNPs) and dinucleotide repeat markers in the 15q14 linkage region and analyzed based on the presence of particular alleles of the dinucleotide repeat marker D15S165 in the 15q14 region. Two alleles showed both familial transmission disequilibrium and population-wide association with schizophrenia. The two groups identified by these two D15S165 alleles differ in age of onset, number of hospitalizations and intensity of nicotine abuse, as well as in predominant ethnicity. Variations in the frequency of SNPs in CHRNA7, the alpha-7-nicotinic acetylcholine receptor subunit gene at 15q14, were found in each group. Further sequencing in these two groups may yield more definitive identification of the molecular pathology.

Differential modulation of gene expression in the NMDA postsynaptic density of schizophrenic and control smokers

Nicotine is known to induce the release of multiple neurotransmitters, including glutamate and dopamine, through activation of nicotinic receptors. Gene expression in the N-methyl-d-aspartate postsynaptic density (NMDA-PSD), as well as other functional groups, was compared in postmortem hippocampus of schizophrenic and nonmentally ill smokers and nonsmokers utilizing a microarray and quantitative RT-PCR approach. The expression of 277 genes was significantly changed between all smokers and nonsmokers. Specific gene groups, most notably genes expressed in the NMDA-PSD, were prevalent among these transcripts. Analysis of the interaction between smoking and schizophrenia identified several genes in the NMDA-PSD that were differentially affected by smoking in patients. The present findings suggest that smoking may differentially modulate glutamatergic function in schizophrenic patients and control subjects. The biological mechanisms underlying chronic tobacco use are likely to differ substantially between these two groups.

Induction of murine spiral artery modification by recombinant human interferon-gamma

Functions of uterine natural killer (uNK) cells during mouse pregnancy are maintenance of decidua basalis and promotion of uterine spiral artery modification, a process that results in thin-walled, dilated, elongated arteries with lowered resistance. Murine models indicate spiral artery modifications are triggered by release of the cytokine interferon (IFN)-gamma from uNK cells. The purpose of this study was to determine if human IFN-gamma could induce structural changes in the unmodified spiral arteries found in pregnant, alymphoid (uNK-, NK-, T-, B-) mice. Spiral arteries in pregnant Rag2 null/common cytokine chain (c) gamma null mice were modified, in a dose response manner, by daily injections of rhIFN-gamma. Administration of low dose LPS did not induce morphologically recognized structural changes. These findings are key in building humanized murine models of pregnancy since they suggest Rag2 null/gammac null mice provide a bioassay system that would detect the functioning of human uNK cells under in vivo conditions.

Effects of the Osteopontin Gene Variants on Milk Production Traits in Dairy Cattle

Osteopontin (OPN) is a highly phosphorylated glycoprotein whose gene has been cloned and sequenced in different species. Several whole genome scans have identified quantitative trait loci (QTL) affecting milk production traits on bovine chromosome 6 close to the osteopontin gene (OPN) location. The presence of OPN in milk and its elevated expression in mammary gland epithelial cells together with previous QTL studies have prompted us to investigate the effects of OPN variants on milk production traits in the Holstein dairy cattle population. A single nucleotide polymorphism in intron 4 (C/T) was detected and primers were designed to amplify genomic DNA from 1362 bulls obtained from Cooperative Dairy DNA Repository and from 214 cows from the University of Wisconsin herd. For the Repository population, the C allele was associated with an increase in milk protein percentage and milk fat percentage. Correlation between milk protein percentage and milk fat percentage was about 0.57. For the University of Wisconsin herd, the estimates of the effects of allele C were in the same direction as for the Repository population, although these estimates did not reach statistical significance. Our results are consistent with other studies that showed a significant association of the microsatellite markers in the region of OPN with milk protein percentage and other correlated traits.

Parturition following transfer of embryos produced in two media under two oxygen concentrations

In vitro-produced blastocysts were transferred singly to 99 Angus crossbred recipients. Culture treatments were a 2 x 2 factorial of medium (KSOM or SOF) and oxygen concentration (5 or 20%). At parturition, birth weight and frame measurement before colostrum intake were recorded. Fetal membranes were collected; distribution and diameter of cotyledons was recorded. Cotyledon surface area was calculated. Culture with 5% O2 tended to yield smaller birth weights than culture with 20% O2 (39.7+/-1.3 kg versus 43.1+/-1.4 kg; P < 0.1); this effect was pronounced in KSOM, suggesting a medium by oxygen interaction (P < 0.1). When expressed on a body weight basis, calves born following culture with 20% O2 had consistently smaller skeletal measurements than those from culture with 5% O2. Culture with 20% O2 significantly increased individual cotyledon areas both overall and in the fetal horn and cotyledon surface area in the fetal horn. Overall, individual cotyledons were 32% larger when culture involved 20% O2 versus 5% O2; in the fetal horn the increase was 49%. Cotyledon surface area was greater for 20% compared to 5% O2 culture, though a medium by oxygen interaction was also significant (P < 0.05). Cotyledon surface area in the nonfetal horn was greater for KSOM fetal membranes than those from culture in SOF. There was a significant medium by oxygen interaction for total cotyledon number. These data demonstrate culture system-specific effects on calf and fetal membrane traits.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

Thirty-day mortality from colorectal cancer surgery within a deprived population

OBJECTIVE

A recently published model for predicting 30-day mortality has been devised using data from 73 hospitals in the UK. Deprivation category was not one of the data sets used in predicting mortality and was not included in formulating this model. We wished to assess if the model was applicable to a population with high deprivation category scores.

METHODS

Data on all colorectal cancer operations included in the model (age, ASA, cancer resected, Dukes stage and urgency) had been collected prospectively since January 1999. This data was applied to the model.

RESULTS

Two hundred and thirty patients were included in analysis. Overall predicted mortality was 8.2% and actual mortality 7.8%. Within different categories of deprivation, predicted and actual mortality are similar and not significantly different. 137 patients lived in areas of deprivation category 3-5. Predicted and actual mortality were 8.4% and 8.0%, respectively. In areas of deprivation category 6-7, 91 patients had a predicted and actual mortality of 8.0% and 7.7%.

CONCLUSION

Although deprivation data was not included in the production of the mathematical model to predict postoperative death, the model appears to predict well in the deprived population. It is likely that poorer socio-economic status is accounted for by increased ASA and cancer stage.

Ovum pick up and in vitro embryo production in cows superstimulated with an individually adapted superstimulation protocol

The aim of this experiment was to apply an ovarian superstimulation protocol prior to ovum pick up (OPU), tailored to the individual donor response, to evaluate its advantages and disadvantages in terms of follicle numbers and diameters, the numbers of retrieved oocytes and day 7 cultured blastocysts. Ten adult non-lactating dairy cows were superstimulated with pFSH and subjected to ovum pick up-in vitro fertilisation (OPU-IVF) 6 times at 2-week intervals. On day 0 of each 2-week period, all follicles >8mm were ablated and an ear implant (Crestar, Intervet, Belgium) was inserted. On day 2, 48 h after follicle ablation the animals were administered six equal doses of pFSH, divided into morning and evening doses for 3 days. On day 7, 48 h following the last pFSH injection, follicle diameters were measured by ultrasound and all follicles were subjected to OPU. All cumulus-oocyte complexes (COC), regardless of their quality, were subjected to in vitro maturation-in vitro fertilisation-in vitro culture (IVM-IVF-IVC). The total dose of pFSH prior to the first OPU session was 300 microg per animal. During the following OPU sessions, the total pFSH dose was either kept unchanged, increased or reduced (+/-50 microg), according to the percentage of follicles of more than 11 mm in diameter, present in the previous session of that particular donor. The mean number of punctured follicles per session was 11.9 +/- 7.7 (mean +/- S.D.), with 16% of follicles exceeding 11 mm. These follicles yielded a mean of 5.6 +/- 4.1 cumulus oocyte complexes (COC), 32% of which had >/=3 layers of cumulus cells (quality 1 and 2). The recovery rate was 47%. Finally, all COC were subjected to IVM-IVF-IVC, which resulted in a mean of 2.0 +/- 2.3 blastocysts on day 7 postinsemination. The subtle changes in pFSH dose influenced the sizes but not the numbers of follicles, the latter parameter was influenced by the individual donor and the OPU session.