Reward ignorant modeling of dynamic treatment regimes

Personalized medicine optimizes patient outcome by tailoring treatments to patient‐level characteristics. This approach is formalized by dynamic treatment regimes (DTRs): decision rules that take patient information as input and output recommended treatment decisions. The DTR literature has seen the development of increasingly sophisticated causal inference techniques that attempt to address the limitations of our typically observational datasets. Often overlooked, however, is that in practice most patients may be expected to receive optimal or near‐optimal treatment, and so the outcome used as part of a typical DTR analysis may provide limited information. In light of this, we propose considering a more standard analysis: ignore the outcome and elicit an optimal DTR by modeling the observed treatment as a function of relevant covariates. This offers a far simpler analysis and, in some settings, improved optimal treatment identification. To distinguish this approach from more traditional DTR analyses, we term it reward ignorant modeling, and also introduce the concept of multimethod analysis, whereby different analysis methods are used in settings with multiple treatment decisions. We demonstrate this concept through a variety of simulation studies, and through analysis of data from the International Warfarin Pharmacogenetics Consortium, which also serve as motivation for this work.     

Electron microscopy and restriction enzyme mapping reveal additional intervening sequences in the chicken ovalbumin split gene

The Eco RI fragment “b” of chicken DNA (Breathnach, Mandel and Chambon, 1977), which contains the sequences coding for the 5′ quarter of ovalbumin mRNA (ov mRNA), has been isolated by molecular cloning using a “shotgun” approach. Electron microscopy and restriction enzyme analysis have revealed that the sequences coding for the 5′ quarter (～500 nucleotides) of ov mRNA are split into four regions separated by three intervening sequences. The cloning procedure seems to be reliable, since the restriction enzyme pattern of the cloned Eco RI fragment “b” is similar to that of the corresponding chromosomal DNA fragment. There is no evidence supporting the existence of a 150–200 nucleotide long sequence at the 5′ end of the ov mRNA similar to the “leader” sequences found at the 5′ end of some adenovirus and SV40 mRNAs.     

Does Aging Have a Purpose?

Ideas of proponents and opponents of programmed aging concerning the expediency of this phenomenon for the evolution of living organisms are briefly considered. We think that evolution has no “gerontological” purpose, because the obligate restriction of cell proliferation during the development of multicellular organisms is a factor that “automatically” triggers aging due to the accumulation of various macromolecular lesions in cells as a result of the suppression, or even complete cessation of emergence of new, intact cells. This leads to the “dilution” of stochastic damage (the most important of which is DNA damage) at the level of the entire cellular population. Some additional arguments in favor of the inexpediency of aging for both species and individuals are also listed.     

Intrinsic Disorder in the Protein Data Bank

Abstract

The Protein Data Bank (PDB) is the preeminent source of protein structural information. PDB contains over 32,500 experimentally determined 3-D structures solved using X-ray crystallography or nuclear magnetic resonance spectroscopy. Intrinsically disordered regions fail to form a fixed 3-D structure under physiological conditions. In this study, we compare the amino-acid sequences of proteins whose structures are determined by X-ray crystallography with the corresponding sequences from the Swiss-Prot database. The analyzed dataset includes 16,370 structures, which represent 18,101 PDB chains and 5,434 different proteins from 910 different organisms (2,793 eukaryotic, 2,109 bacterial, 288 viral, and 244 archaeal). In this dataset, on average, each Swiss-Prot protein is represented by 7 PDB chains with 76% of the crystallized regions being represented by more than one structure. Intriguingly, the complete sequences of only ~7% of proteins are observed in the corresponding PDB structures, and only ~25% of the total dataset have >95% of their lengths observed in the corresponding PDB structures. This suggests that the vast majority of PDB proteins is shorter than their corresponding Swiss-Prot sequences and/or contain numerous residues, which are not observed in maps of electron density. To determine the prevalence of disordered regions in PDB, the residues in the Swiss-Prot sequences were grouped into four general categories, “Observed” (which correspond to structured regions), “Not observed” (regions with missing electron density, potentially disordered), “Uncharacterized,” and “Ambiguous,” depending on their appearance in the corresponding PDB entries. This non-redundant set of residues can be viewed as a ‘fragment’ or empirical domain database that contains a set of experimentally determined structured regions or domains and a set of experimentally verified disordered regions or domains. We studied the propensities and properties of residues in these four categories and analyzed their relations to the predictions of disorder using several algorithms. “Non-observed,” “Ambiguous,” and “Uncharacterized” regions were shown to possess the amino acid compositional biases typical of intrinsically disordered proteins. The application of four different disorder predictors (PONDR® VL-XT, VL3-BA, VSL1P, and IUPred) revealed that the vast majority of residues in the “Observed” dataset are ordered, and that the “Not observed” regions are mostly disordered. The “Uncharacterized” regions possess some tendency toward order, whereas the predictions for the short “Ambiguous” regions are really ambiguous. Long “Ambiguous” regions (>70 amino acid residues) are mostly predicted to be ordered, suggesting that they are likely to be “wobbly” domains.

Overall, we showed that completely ordered proteins are not highly abundant in PDB and many PDB sequences have disordered regions. In fact, in the analyzed dataset ~10% of the PDB proteins contain regions of consecutive missing or ambiguous residues longer than 30 amino-acids and ~40% of the proteins possess short regions (≥10 and <30 amino-acid long) of missing and ambiguous residues.     

基于中华鲟繁殖群体数量的长江中、下游生态环境考核指标

繁殖群体数量是中华鲟能否成功繁殖的重要影响因子, 建议作为长江生态考核的重要评价指标。根据重要种群参数和历史数据, 基于稳态转换理论和方法, 确定中华鲟繁殖群体数量指标的评估基准值和等级, 670尾以上为“优”、400—670尾为“良”、200—400尾为“中”、50—200尾为“差”、50尾以下为“极差”。水声学探测结果显示, 1998—2001年中华鲟繁殖群体数量指标评级为“良”; 2004—2012年三峡工程蓄水后至向家坝蓄水前评级为“中”; 2013—2020年评级为“极差”。为了复壮中华鲟野生种群, 建议修复葛洲坝下中华鲟产卵场功能, 大规模放流性成熟亲鱼和大规格个体, 建立国家级中华鲟保育中心。     

Inter-colonial incompatibility and aggressive interactions inPristomyrmex pungens (Hymenoptera: Formicidae)

Previous workers (Tsuji & Itô 1986) have presented evidence that suggests individuals of the Japanese queenless ant,Pristomyrmex pungens (Formicidae, Myrmicinae) which is an obligatorily thelytokous species, can recognize individuals of “home” and those of “other” colonies. The data presented here are derived from an improved experimental set (transfer between foraging areas) and support the existence of colony recognition mechanisms. I also present some data on “natural” inter-colony interactions observed in the field. The studied population was divided into many distinct colonies (they were not unicolonial) and inter-colonial exchange was considered to be inhibited by aggressive interactions during inter-colonial encouters. During encounters between individuals from different colonies, fighting was often observed, and sometimes resulted in the death of combatants. Dead or wounded combatants were never carried into the nest of the winner's colony.     

International Society for Cell & Gene Therapy Stem Cell Engineering Committee: Cellular therapies for the treatment of graft-versus-host-disease after hematopoietic stem cell transplant

Background aimsAllogeneic hematopoietic stem cell transplant is a curative approach for many malignant and non-malignant hematologic conditions. Despite advances in its prevention and treatment, the morbidity and mortality related to graft-versus-host disease (GVHD) remains. The mechanisms by which currently used pharmacologic agents impair the activation and proliferation of potentially alloreactive T cells reveal pathways essential for the detrimental activities of these cell populations. Importantly, these same pathways can be important in mediating the graft-versus-leukemia effect in recipients transplanted for malignant disease. This knowledge informs potential roles for cellular therapies such as mesenchymal stromal cells and regulatory T cells in preventing or treating GVHD. This article reviews the current state of adoptive cellular therapies focused on GVHD treatment.MethodsWe conducted a search for scientific literature in PubMed® and ongoing clinical trials in clinicaltrial.gov with the keywords “Graft-versus-Host Disease (GVHD),” “Cellular Therapies,” “Regulatory T cells (Tregs),” “Mesenchymal Stromal (Stem) Cells (MSCs),” “Natural Killer (NK) Cells,” “Myeloid-derived suppressor cells (MDSCs),” and “Regulatory B-Cells (B-regs).” All the published and available clinical studies were included.ResultsAlthough most of the existing clinical data focus on cellular therapies for GVHD prevention, there are observational and interventional clinical studies that explore the potential for cellular therapies to be safe modalities for GVHD treatment while maintaining the graft-versus-leukemia effect in the context of malignant diseases. However, there are multiple challenges that limit the broader use of these approaches in the clinical scenario.ConclusionsThere are many ongoing clinical trials to date with the promise to expand our actual knowledge on the role of cellular therapies for GVHD treatment in an attempt to improve GVHD-related outcomes in the near future.     

Individual differences in behaviour explain variation in survival: a meta‐analysis

Research focusing on among‐individual differences in behaviour (‘animal personality’) has been blooming for over a decade. Central theories explaining the maintenance of such behavioural variation posits that individuals expressing greater “risky” behaviours should suffer higher mortality. Here, for the first time, we synthesize the existing empirical evidence for this key prediction. Our results did not support this prediction as there was no directional relationship between riskier behaviour and greater mortality; however there was a significant absolute relationship between behaviour and survival. In total, behaviour explained a significant, but small, portion (5.8%) of the variance in survival. We also found that risky (vs. “shy”) behavioural types live significantly longer in the wild, but not in the laboratory. This suggests that individuals expressing risky behaviours might be of overall higher quality but the lack of predation pressure and resource restrictions mask this effect in laboratory environments. Our work demonstrates that individual differences in behaviour explain important differences in survival but not in the direction predicted by theory. Importantly, this suggests that models predicting behaviour to be a mediator of reproduction‐survival trade‐offs may need revision and/or empiricists may need to reconsider their proxies of risky behaviours when testing such theory.     

Next-generation phylogenomics using a Target Restricted Assembly Method

Next-generation sequencing technologies are revolutionizing the field of phylogenetics by making available genome scale data for a fraction of the cost of traditional targeted sequencing. One challenge will be to make use of these genomic level data without necessarily resorting to full-scale genome assembly and annotation, which is often time and labor intensive. Here we describe a technique, the Target Restricted Assembly Method (TRAM), in which the typical process of genome assembly and annotation is in essence reversed. Protein sequences of phylogenetically useful genes from a species within the group of interest are used as targets in tblastn searches of a data set from a lane of Illumina reads for a related species. Resulting blast hits are then assembled locally into contigs and these contigs are then aligned against the reference “cDNA” sequence to remove portions of the sequences that include introns. We illustrate the Target Restricted Assembly Method using genomic scale datasets for 20 species of lice (Insecta: Psocodea) to produce a test phylogenetic data set of 10 nuclear protein coding gene sequences. Given the advantages of using DNA instead of RNA, this technique is very cost effective and feasible given current technologies.     

Delimitation of evolutionary units in Cuvier’s dwarf caiman, <Emphasis Type="Italic">Paleosuchus palpebrosus</Emphasis> (Cuvier, 1807): insights from conservation of a broadly distributed species

An important goal of evolutionary and conservation biology is the identification of units below the species level, such as Evolutionarily Significant Units (ESUs), providing objectively delimited units for species conservation and management. In this study we tested the hypothesis that Cuvier’s dwarf caiman (Paleosuchus palpebrosus)—a species broadly distributed across several biomes and watersheds of South America—is comprised of different ESUs. We analyzed mitochondrial cytochrome b sequences of 206 individuals and 532 unlinked ddRAD loci of 20 individuals chosen from amongst the mitochondrial haplogroups. Analysis of the cytochrome b sequences revealed four mitochondrial clusters, while STRUCTURE analysis of ddRAD loci detected three genomic clusters with different levels of mixture between them. Using the Adaptive Evolutionary Conservation (AEC) framework we identified three ESUs: “Amazon”, “Madeira-Bolivia” and “Pantanal”; one of them composed of two different Management Units (MUs), “Madeira” and “Bolivia”. In general, based on the comparisons with other crocodilian species, genetic diversity of each lineage was moderate however, the Madeira MU showed fivefold lower genetic diversity than other geographic groups. Considering the particularities of each Paleosuchus palpebrosus conservation unit, we recommend that the conservation status of each is evaluated separately. Tropical biodiversity is largely underestimated and in this context the broadly distributed species are the most likely candidates to harbor distinct evolutionary lineages. Thus, we suggest that conservation research should not neglect species that are generally considered of Least Concern by IUCN due to the taxon’s broad geographic distribution.     

Model selection for G‐estimation of dynamic treatment regimes

Dynamic treatment regimes (DTRs) aim to formalize personalized medicine by tailoring treatment decisions to individual patient characteristics. G‐estimation for DTR identification targets the parameters of a structural nested mean model, known as the blip function, from which the optimal DTR is derived. Despite its potential, G‐estimation has not seen widespread use in the literature, owing in part to its often complex presentation and implementation, but also due to the necessity for correct specification of the blip. Using a quadratic approximation approach inspired by iteratively reweighted least squares, we derive a quasi‐likelihood function for G‐estimation within the DTR framework, and show how it can be used to form an information criterion for blip model selection. We outline the theoretical properties of this model selection criterion and demonstrate its application in a variety of simulation studies as well as in data from the Sequenced Treatment Alternatives to Relieve Depression study.     

Organization and evolutionary progress of a dispersed repetitive family of sequences in widely separated rodent genomes

The genomes of Mus musculus and other rodent species share a long conserved family of sequences that are dispersed and abundant (approx. 20,000 copies), and that have several novel features of organization and evolution. EcoR1 restriction of M. musculus DNA reveals a prominent 1350 bp² set of sequences. Two nonhomologous sequences of 850 and 500 bp, representing almost the total population of the 1350 bp repeats, were used to examine the detailed organization of the dispersed family and its surrounding sequences using a combination of restriction analysis and “Southern” hybridization. The 1350 bp sequence is contained within a longer repeating unit of approximately 3 kb that is dispersed amongst a wide variety of non-homologous and seemingly non-repetitive sequences. At some sites within the 3 kb repeat, considerable sequence heterogeneity has been found between members of the family, such that the family can be divided into largely non-overlapping subsets (or “segments”) according to the positioning of HinIII sites. Underlying the segmental organization there is a low background overlap of each segment with every other. Some but not all members of the family and its variants have been located on the X-chromosome in a Chinese hamster, M. musculus, X chromosome cell line: suggesting a wide genomic dispersion of the family. Homologous repeated sequences to the M. musculus 1350 bp repeat have been identified in species of Mus and Apodemus, with strikingly similar features of organization and dispersion. In M. spretus a 1350 bp sequence is contained within a dispersed repeat of at least 2·9 kb. However, the majority of M. spretus repeats contain an additional restriction site not present in the equivalent M. musculus array, suggesting a mechanism of widespread substitution or “conversion” of one variant by another in each genome. Apodemus sylvaticus possesses two dispersed and homologous families of 1350 bp and 1850 bp repetition, respectively, which contain sequences that have diverged from M. musculus to differing extents. A. mystacinus possesses only one family of dispersed and homologous repeats of 1850 bp. The majority of members within each Apodemus homologous family also contain characteristic variant restriction-site arrangements. The mechanisms underlying the spread of such variants within each array; the generation of segmental patterns; and the evolutionary conservation of this mouse interspersed family (MIF-1) are discussed in relation to the present knowledge of the organization and activity of other dispersed sequence families.     

Identification and classification of a resistance breaking strain of barley yellow mosaic virus

A “resistance breaking” isolate of barley yellow mosaic virus-2 (BaYMV-2) was cloned as a cDNA and characterised. Restriction mapping and comparison with a German and a Japanese isolate of BaYMV (BaYMV-G and BaYMV-J) revealed a high level of restriction site conservation for RNAl and the majority of RNA2. However, in a box of approximately 600 nucleotides located on RNA2, striking differences in the restriction pattern could be identified. The nucleotide sequence of this box, as well as of the 3‘-terminal region of RNA1 including the coat protein coding region, and the deduced amino acid sequences were analysed. Identity at the amino acid level was between 99.3% and 92.3% in comparison with the corresponding sequences of BaYMV-G and BaYMV-J, suggesting that BaYMV-2 is closely related to BaYMV. Consequently, the classification of BaYMV-2 as a “resistance breaking” strain of BaYMV is justified.     

A Robust Method for Estimating Optimal Treatment Regimes

Summary A treatment regime is a rule that assigns a treatment, among a set of possible treatments, to a patient as a function of his/her observed characteristics, hence “personalizing” treatment to the patient. The goal is to identify the optimal treatment regime that, if followed by the entire population of patients, would lead to the best outcome on average. Given data from a clinical trial or observational study, for a single treatment decision, the optimal regime can be found by assuming a regression model for the expected outcome conditional on treatment and covariates, where, for a given set of covariates, the optimal treatment is the one that yields the most favorable expected outcome. However, treatment assignment via such a regime is suspect if the regression model is incorrectly specified. Recognizing that, even if misspecified, such a regression model defines a class of regimes, we instead consider finding the optimal regime within such a class by finding the regime that optimizes an estimator of overall population mean outcome. To take into account possible confounding in an observational study and to increase precision, we use a doubly robust augmented inverse probability weighted estimator for this purpose. Simulations and application to data from a breast cancer clinical trial demonstrate the performance of the method.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

On optimal nonlinear associative recall

The problem of determining the nonlinear function (“blackbox”) which optimally associates (on given criteria) two sets of data is considered. The data are given as discrete, finite column vectors, forming two matricesX (“input”) andY (“output”) with the same numbers of columns and an arbitrary numbers of rows. An iteration method based on the concept of the generalized inverse of a matrix provides the polynomial mapping of degreek onX by whichY is retrieved in an optimal way in the least squares sense. The results can be applied to a wide class of problems since such polynomial mappings may approximate any continuous real function from the “input” space to the “output” space to any required degree of accuracy. Conditions under which the optimal estimate is linear are given. Linear transformations on the input key-vectors and analogies with the “whitening” approach are also discussed. Conditions of “stationarity” on the processes of whichX andY are assumed to represent a set of sample sequences can be easily introduced. The optimal linear estimate is given by a discrete counterpart of the Wiener-Hopf equation and, if the key-signals are noise-like, the holographic-like scheme of associative memory is obtained, as the optimal nonlinear estimator. The theory can be applied to the system identification problem. It is finally suggested that the results outlined here may be relevant to the construction of models of associative, distributed memory.     

Individual heterogeneity in reproductive rates and cost of reproduction in a long‐lived vertebrate

Individual variation in reproductive success is a key feature of evolution, but also has important implications for predicting population responses to variable environments. Although such individual variation in reproductive outcomes has been reported in numerous studies, most analyses to date have not considered whether these realized differences were due to latent individual heterogeneity in reproduction or merely random chance causing different outcomes among like individuals. Furthermore, latent heterogeneity in fitness components might be expressed differently in contrasted environmental conditions, an issue that has only rarely been investigated. Here, we assessed (i) the potential existence of latent individual heterogeneity and (ii) the nature of its expression (fixed vs. variable) in a population of female Weddell seals (Leptonychotes weddellii), using a hierarchical modeling approach on a 30‐year mark–recapture data set consisting of 954 individual encounter histories. We found strong support for the existence of latent individual heterogeneity in the population, with “robust” individuals expected to produce twice as many pups as “frail” individuals. Moreover, the expression of individual heterogeneity appeared consistent, with only mild evidence that it might be amplified when environmental conditions are severe. Finally, the explicit modeling of individual heterogeneity allowed us to detect a substantial cost of reproduction that was not evidenced when the heterogeneity was ignored.     

Total synthesis of multi-kilobase DNA sequences from oligonucleotides

A method for synthesizing DNA from 40-mer oligonucleotides, which we used to generate a 32-kb DNA fragment, is explained. DNA sequences are synthesized as approximately 500 bp fragments (synthons) in a two-step PCR reaction and cloned using ligation-independent cloning (LIC). Synthons are then assembled into longer full-length sequences in a stepwise manner. By initially synthesizing smaller fragments (synthons), the number of clones sequenced is low compared with synthesizing complete multi-kilobase DNA sequences in a single step. LIC eliminates the need for purification of fragments before cloning, making the process amenable to high-throughput operation and automation. Type IIs restriction enzymes allow seamless assembly of synthons without placing restrictions on the sequence being synthesized. Synthetic fragments are assembled in pairs to generate the final construct using vectors that allow selection of desired clones with two unique antibiotic resistance markers, and this eliminates the need for purification of fragments after digestion with restriction endonucleases.     

Multivariate assessments of activity-related skeletal changes: Interpreting Bell Beaker specialized male archery and social organization in Central Europe

Objectives

The Bell Beaker period witnessed the rise of individual inhumations with “wealthy” burial contexts containing archery-related grave goods, leading archaeologists to label the individuals in these tombs as “archers.” This study looks to (1) compare the skeletons from male “archer” burials with those from male “non-archer” burials—those not having archery-related grave goods—in order to assess a possible link between burial context and physical activity, and (2) apply a biomechanics profile to evaluate whether the individuals associated with these “archer” burials practiced specialized archer activity.

Materials and Methods

The corpus (males only) included 46 “archers” and 40 “non-archers” from Bell Beaker individual inhumations. Osteological data included measurements, scores of entheseal changes, and a diagnosis of certain pathologies. Data analyses involved visual observations, hypothesis tests, dimension reduction, and MANOVA, with approaches aimed at exploring the treatment of data missingness.

Results

Measurement data revealed no differences between the two groups. Evaluations of entheseal changes found that “non-archers” had consistently more instances of bone surface modifications than “archers.” Individual assessments of specialized archer occupation identified 11 possible specialized archers.

Discussion

These findings indicate a possible labor differentiation represented through the presence of a probably prestigious “archer” burial context. This suggests a link between grave good presence and labor, but not between a Bell Beaker archery occupation and an “archer” burial context. Data analyses support the application of biomechanics to osteological analyses in order to assess specialized activity on the skeleton.