Scale-free dynamics of COVID-19 in a Brazilian city.

A common basis to address the dynamics of directly transmitted infectious diseases, such as COVID-19, are compartmental (or SIR) models. SIR models typically assume homogenous population mixing, a simplification that is convenient but unrealistic. Here we validate an existing model of a scale-free fractal infection process using high-resolution data on COVID-19 spread in São Caetano, Brazil. We find that transmission can be described by a network in which each infectious individual has a small number of susceptible contacts, of the order of 2-5. This model parameter correlated tightly with physical distancing measured by mobile phone data, such that in periods of greater distancing the model recovered a lower average number of contacts, and vice versa. We show that the SIR model is a special case of our scale-free fractal process model in which the parameter that reflects population structure is set at unity, indicating homogeneous mixing. Our more general framework better explained the dynamics of COVID-19 in São Caetano, used fewer parameters than a standard SIR model and accounted for geographically localized clusters of disease. Our model requires further validation in other locations and with other directly transmitted infectious agents.

Performance and visceral tissue growth and development of Holstein calves fed differing milk replacer allowances and starch concentrations in pelleted starter.

The objectives of this study were to investigate how milk replacer (MR) allowance and differing concentrations of starch and neutral detergent fiber in starter alters visceral tissue and overall growth of the calf. Calves were randomly assigned to 1 of 4 dietary treatments (n = 12 per treatment) arranged in a 2 × 2 factorial based on daily MR allowance (MRA) and amount of starch in pelleted starter (SPS) as follows: 0.691 kg of MR/d [dry matter (DM) basis] with starter containing low or high starch (12.0% and 35.6% starch, respectively) and 1.382 kg of MR/day (DM) with starter containing low or high starch. All calves were housed in individual pens with straw bedding until wk 5 when bedding was covered to minimize intake. Calves were fed MR twice daily (0700 and 1700 h) containing 24.5% crude protein (DM) and 19.8% fat (DM), and had access to pelleted starter (increased by 50 g/d if there were no refusals before weaning, and then 200 g/d during and after weaning) and water starting on d 1. Calves arrived between 1 and 3 d of age and were enrolled into an 8-wk study, with calves undergoing step-down weaning during wk 7. Intakes were measured daily, and body weight (BW) and blood samples were recorded and collected weekly. Calves were dissected in wk 8 for visceral tissue measurements. Overall, there was increased MR DM intake for the high- (0.90 ± 0.01 kg/d; ± SE) compared with the low-MRA (0.54 ± 0.01 kg/d) calves, whereas starter DM intake increased in low- (0.47 ± 0.05 kg/d) compared with high-MRA (0.20 ± 0.05 kg/d) calves, which was driven by increases in wk 6, 7, and 8. High-MRA calves had increased BW during wk 2, 3, 4, 5, 6, and 7. The difference in BW disappeared by wk 8, with overall average daily gain having a tendency to be increased in high (0.57 ± 0.04 kg/d) compared with low-MRA (0.50 ± 0.04 kg/d) calves, whereas average daily gain was increased in high-MRA calves during wk 2 and 3 and increased in low-MRA calves during wk 7 and 8. There were several differences throughout visceral tissue measurements, but most notably, an increase in rumen mass (i.e., full, empty, and digesta weights) in low- compared with high-MRA calves, as well as in low- compared with high-SPS calves was observed. The length, width, and 2-dimensional area of rumen papillae were also increased in low- (area: 0.88 ± 0.03 mm2) compared with high-MRA (0.46 ± 0.03 mm2) calves. The majority of differences were attributed to increased MR allowance, which contributed to reduced pelleted starter intake by more than 50% and reduced rumen development, whereas differences in starch intake from the completely pelleted starter had minimal effects on overall growth and tissue measurements.

The effect of neomycin inclusion in milk replacer on the health, growth, and performance of male Holstein calves during preweaning.

The prophylactic use of oral antimicrobials, such as neomycin, in milk replacer (MR) or whole milk is a common practice in calf-rearing that is thought to aid in preventing disease. Heavy reliance on antimicrobials is of concern not only because of the development of antimicrobial resistance, but also because of the potentially negative effects on health. The objective of this study was to investigate the effects of neomycin on calf health and growth performance. One hundred and sixty calves (approximately 3-10 d of age), distributed across 2 experimental periods, were stratified by body weight (BW) and serum total protein, and assigned to 1 of 3 treatments: control (CON; nonmedicated MR, n = 60), short-term antibiotic (ST; neomycin mixed in MR from d 1-14, n = 50), or long-term antibiotic (LT; neomycin in ​MR from d 1-28, n = 50). Arrival BW (47.69 ± 0.87 kg) and serum total protein (5.67 ± 0.09 g/dL) were not different between treatment groups. Neomycin in ST and LT was dosed in MR at a rate of 20 mg/kg of BW and was adjusted weekly according to BW. Calf BW was measured weekly for 49 d, and health indicators (fecal score, attitude score, respiratory score, and rectal temperature), MR intake, starter intake, and the use of additional electrolytes and antimicrobials were recorded daily. Calves in the CON group experienced a higher proportion of days with diarrhea (20.32 ± 0.02%) compared with ST (14.70 ± 0.02%) or LT (13.80 ± 0.02%) calves, as well as longer bouts of diarrhea (7.45 ± 0.38 d, 5.69 ± 0.46 d, and 5.62 ± 0.45 d for CON, ST, and LT calves, respectively). Calves in the CON group also experienced higher fecal scores (score of 0.64 ± 0.04) than ST (score of 0.53 ± 0.04) or LT (score of 0.49 ± 0.04) calves, especially at d 7. However, no differences were observed in other health-related measures. The time to reach first diarrhea and first respiratory illness was not different between treatments, nor was the time to recover from respiratory illness. The time to intervention with additional electrolytes or antimicrobials was not different between treatment groups. Furthermore, growth performance, feed intake, and feed conversion ratio were not different. No differences were found when comparing ST and LT, except in the defined daily dose of total antimicrobials received. Calves in the LT group received a higher overall dose than ST calves, and both ST and LT calves received a higher dose than CON calves, which received no prophylactic antimicrobials. Given that there were no differences in performance variables and no additional health benefits aside from reduced fecal scores in calves fed neomycin, current practices involving the use of antimicrobials on dairy and veal operations need to be considered more prudently.

Technical note: Is fecal consistency scoring an accurate measure of fecal dry matter in dairy calves?

The objective of this cross-sectional study was to evaluate the accuracy of fecal consistency scoring as a measure of fecal dry matter (DM) in dairy calves. This study was conducted at a commercial grain-fed veal facility in southwestern Ontario. A total of 160 calves arrived at the facility in 2 groups of 80 calves each. Calves were fed milk replacer twice daily at 0700 and 1700 h and had ad libitum access from arrival onward to water through nipple drinkers and starter through a shared trough. Fecal consistency scores were evaluated once daily in the first 28 d after arrival before milk feeding. The fecal consistency scoring was conducted using a 4-level scoring scale: 0 = normal (firm but not hard); 1 = soft (does not hold form, piles but spreads slightly); 2 = runny (spreads readily); and 3 = watery (liquid consistency, splatters). Fecal samples were collected from all calves via rectal palpation on d 1, 7, 14, and 21 at 0900 h for determination of fecal DM. Mixed repeated measures linear regression models were built to assess the accuracy of fecal consistency scoring in predicting fecal DM. Over 4 selected time points (d 1, 7, 14, and 21) the 160 calves were observed, 382 (61.6%) had a fecal consistency score of 0, 121 (19.5%) had a score of 1, 85 (13.7%) had a score of 2, and 32 (5.2%) had a score of 3. A fecal score of 0 had a fecal DM of 25.1 ± 8.4%, whereas a fecal score of 1 had a DM of 21.8 ± 8.2%. With respect to calves that had a fecal score of 2 or 3, their fecal DM was 16.0 ± 11.1% and 10.7 ± 6.9%, respectively. In evaluating the pairwise comparisons generated in the repeated measures model that controlled for day of sampling, a fecal score of 0 had a 3.2%, 8.1%, and 12.0% higher fecal DM, respectively, when compared with those that had a fecal score of 1, 2, and 3. In addition, calves with a fecal score of 1 had a 5.0% and 8.8% higher fecal DM than calves with a fecal score of 2 and 3, respectively. Finally, calves with a fecal score of 2 had a 3.8% higher fecal DM than those with a fecal score of 3. This study confirms that using observational fecal consistency scoring can accurately predict diarrhea or a decline in fecal DM.

Viruses and exacerbations of chronic obstructive pulmonary disease: unmet clinical need.

Chronic obstructive pulmonary disease (COPD) is a non-communicable long-term condition characterised by accelerated lung-function decline and intermittent episodes of respiratory illness called exacerbations. We discuss the current understanding of the role of viruses in these elements of COPD. The burden of acute viral illness in COPD is great and largely unrecognised. Because naturally occurring exacerbations are inherently difficult to study, only recently have we understood underlying pathophysiological mechanisms and the true prevalence of viral exacerbations. Data are also emerging to support a potential role for chronic viral infection in the progression of stable COPD. As knowledge in these two areas develops, it is clear that the role of viruses in COPD represents a significant unmet clinical need.

Spontaneous abortion: a prospective cohort study of younger women from the general population in Denmark. Validation, occurrence and risk determinants.

OBJECTIVE: To assess the occurrence of spontaneous abortion, comparing two different data sources. To estimate the rate of spontaneous abortion over a 2-year period, and examine potential predictors of the risk for incident spontaneous abortion. METHODS: We used interview data from a population-based prospective cohort study comprising 11,088 women and data from a linkage of the cohort with the Hospital Discharge Register to compare spontaneous abortions as reported in the interview with those identified in the register. Based on interview data, we estimated the rate of spontaneous abortion during the two-year follow-up. Finally, risk determinants for incident spontaneous abortion were analyzed by means of logistic regression. RESULTS: A total of 654 spontaneous abortions before enrolment in the study were reported by the women compared to 531 abortions found in the register. More than 80% of the spontaneous abortions identified from both sources were recorded in the same year. During follow-up a total of 20.9% of pregnancies intended to be carried to term ended as a spontaneous abortion. In the risk factor analysis, we found that previous spontaneous abortion, being single, never having used oral contraceptives, and use of intrauterine device were associated with increased risk of subsequent spontaneous abortion. In addition, it was indicated that a short interpregnancy interval following a spontaneous abortion may confer an increased risk of abortion in the subsequent pregnancy. CONCLUSION: We found a high rate of spontaneous abortion in the present study and an acceptable agreement between information obtained by interview and register information. More than 25% of the spontaneous abortions were only reported by the women, and this could not be explained by erroneously reported induced abortions, and may be early, nonhospitalized abortions. We confirm that number of previous spontaneous abortions is a strong determinant, and our data may also indicate a role of previous contraceptive habits. A role of the length of interpregnancy interval in the risk of spontaneous abortion cannot be ruled out.

Colony integration and the expression of the Hox gene, Cnox-2, in Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa).

The stolonal mat is an anatomical feature correlated with increased colonial integration in several lineages of the cnidarian class Hydrozoa. Cnox-2 is a Hox gene known to be expressed in the body column of the cnidarian polyp. We report the pattern of Cnox-2 expression in both the stolonal mat and free stolons of the hydroid Hydractinia symbiolongicarpus. The gene is found to have high levels of expression in the mat similar to that found in the basal portion of the polyp, but it is not detectably expressed in those regions of free stolons where polyps are budded. These findings suggest that the stolonal mat arose via an expansion of the basal ectoderm of the polyp.

Expression of a Hox gene, Cnox-2, and the division of labor in a colonial hydroid.

We report the isolation and expression of the Hox gene, Cnox-2, in Hydractinia symbiolongicarpus, a hydrozoan displaying division of labor. We found different patterns of aboral-to-oral Cnox-2 expression among polyp polymorphs, and we show that experimental conversion of one polyp type to another is accompanied by concordant alteration in Cnox-2 expression. Our results are consistent with the suggestion that polyp polymorphism, characteristic of hydractiniid hydroids, arose via evolutionary modification of proportioning of head to body column.

Dynamics of Gastrovascular Circulation in the Hydrozoan Podocoryne carnea: the One-Polyp Case.

Time-lapse video microscopy and image analysis algorithms were used to generate high-resolution time series of the length and volume of a single hydrozoan polyp before and after feeding. A polyp of Podocoryne carnea prior to feeding is effectively static in length and volume. At 20{deg}C, feeding elicits 8-millihertz (mHz) oscillations in polyp length and volume. A polyp connected to a colony by a single stolon displayed an abrupt transition from low-amplitude, 8-mHz oscillations to large-amplitude, 6-mHz oscillations at 1.5-2 h after feeding. The transition was preceded by a substantial decrease in polyp volume and increase in length which coincided with the export of food items from the digestive cavity of the polyp into the colonial gastrovascular system. In contrast, 8-mHz oscillations of a polyp isolated from a colony continued for 12.7 h after feeding, at which time particulates from the digestive cavity were exported into the hydrorhiza and a 4-mHz subharmonic became briefly dominant. Regular oscillatory behavior was terminated by regurgitation at comparable intervals post-feeding in coupled and isolated polyps. These observations are compatible with the hypothesis that the presence of nutrients in the digestive cavity induces polyp oscillations and that release of nutrients into the gastrovascular system similarly induces unfed polyps to oscillate, thereby distributing the contents of the fed polyp throughout the colony.

Over one-half billion years of head conservation? Expression of an ems class gene in Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa).

We report the isolation of an empty spiracles class homeodomain-containing gene, Cn-ems, from the hydrozoan Hydractinia symbiolongicarpus, the first gene of this class characterized in a lower metazoan. Cn-ems was found to be expressed in the head of gastrozooids, specifically in endodermal epithelial cells of the taeniolae of the hypostome. Cn-ems is not expressed in gonozooids, which lack taeniolae. Experimental conversion of the posterior region of the planula larva into head structures up-regulates expression of the gene. These findings establish that the association of ems-class genes with head structures preceded the evolution of bilateral symmetry.

Transmission genetics of allorecognition in Hydractinia symbiolongicarpus (Cnidaria:Hydrozoa).

Allorecognition is ubiquitous, or nearly so, amongst colonial invertebrates. Despite the prominent role that such phenomena have played both in evolutionary theory and in on the origin of the vertebrate immune system, unambiguous data on the transmission genetics of fusibility (i.e., the ability of two individuals to fuse upon tissue contact) is lacking for any metazoan outside of the phylum Chordata. We have developed lines of the hydroid Hydractinia symbiolongicarpus (Phylum Cnidaria) inbred for fusibility and here report results of breeding experiments establishing that fusibility segregates as expected for a single locus with codominantly expressed alleles, with one shared allele producing a fusible phenotype. Surveys of fusibility in field populations and additional breeding experiments indicate the presence of an extensive allele series.

Class-level relationships in the phylum Cnidaria: molecular and morphological evidence.

The evolutionary history of cnidarian life cycles has been debated since the 1880s, with different hypotheses favored even by current textbooks. Contributing to the disagreement is the fact that the systematic relationships of the four cnidarian classes have received relatively little examination using modern systematic methods. Here we present analyses of class-level relationships based on 18S ribosomal DNA (rDNA) sequence, mitochondrial 16S rDNA sequence, mitochondrial genome structure, and morphological characters. DNA sequences were aligned using a repeatable parsimony-based approach incorporating a range of alignment parameters. Analyses of individual data sets and of all data combined are unanimous in grouping the classes possessing a medusa stage, leaving the holobenthic Anthozoa basal within the phylum.

HOM/Hox-type homeoboxes from Stylaria lacustris (Annelida: Oligochaeta).

The polymerase chain reaction was used to survey the oligochaete worm Stylaria lacustris for HOM/Hox type homeobox genes. Twelve fragments were identified and in most cases were assignable to cognate groups on the basis of amino acid similarity. Stylaria appears to have three labial-type genes, a HOX B3 cognate, several genes similar to Antennapedia, and cognates of Abdominal-B and CHox7.

A PCR-based survey of homeobox genes in Ctenodrilus serratus (Annelida: Polychaeta).

The polychaete worm Ctenodrilus serratus was surveyed for the presence of HOM/HOX and engrailed-type homeobox genes using PCR with degenerate primers. Sixteen unique homeobox fragments were found in surveys of genomic and cDNA with three different primer sets. For three fragments, RACE was employed to obtain additional homeobox sequence and the 3' flanking region. Nine HOM/HOX-type fragments were identified, including putative representatives of the Hox1/lab, Hox2/pb, Hox3, Hox4/Dfd, and Antp/Lox5 cognate groups. Two additional Antp-like fragments could not be assigned specific orthology. Presence of an ortholog of leech Lox2 in addition to a Ubx/abdA-like gene suggests that independent duplications of a single precursor occurred in the annelid and arthropod lineages. No representative of the Hox9/AbdB group was identified. Our results are consistent with a hypothesis of a single HOM/HOX cluster in Ctenodrilus as extensive as that seen in strongly tagmatized arthropods, suggesting that the primitive role of these genes even in overtly metameric animals was something other than specification of overt segmental differentiation. The primers used also detected representatives of six other homeobox classes or families: Xlox (XlHbox8/HTr-A2), Ovx (Chox7), caudal, Prh (proline-rich homeobox), NEC (ceh-9/Tghbox5), and engrailed.

What would be conserved if "the tape were played twice"?

We develop an abstract chemistry, implemented in a lambda-calculus-based modeling platform, and argue that the following features are generic to this particular abstraction of chemistry; hence, they would be expected to reappear if "the tape were run twice": (i) hypercycles of self-reproducing objects arise; (ii) if self-replication is inhibited, self-maintaining organizations arise; and (iii) self-maintaining organizations, once established, can combine into higher-order self-maintaining organizations.

HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus.

The polymerase chain reaction was used to survey HOM/Hox type homeobox genes in the North American horseshoe crab, Limulus polyphemus. The survey reveals 28 different homeobox fragments possessing 44-80% nucleotide sequence similarity with HOM-C sequences in Drosophila and Hox B sequences in mouse. Limulus has one to four representatives of HOM/Hox cognates when fragments are assigned according to amino acid identity. A parsimony analysis including the Limulus sequences and homologous mouse Hox B and Drosophila HOM-C sequences reveals several instances of monophyletic groupings of Limulus homeoboxes with a Drosophila or mouse gene as the sister branch. Under the current model of HOM/Hox cluster evolution, these results suggest that Limulus has as many as four HOM/Hox type clusters. This is the first evidence suggesting the presence of multiple clusters in a nonvertebrate taxon. Putative homologs of mouse Hoxb-3 in Limulus suggest that the gene was present in the common ancestor of arthropods and vertebrates and has been lost in Drosophila.

Determination of paternity in dragonflies by Random Amplified Polymorphic DNA fingerprinting.

We used Random Amplified Polymorphic DNA (RAPD) fingerprinting to address issues of paternity in two odonate species. Amplification artifacts of RAPD markers were controlled by assessing paternity patterns relative to the banding patterns generated by quantitative mixtures of DNA from putative parents ('synthetic offspring'). In the aeshnid dragonfly Anax parthenope, for which the mating histories of both males and females were unknown, we found strong evidence for complete paternity success for the contact guarding male. In the highly polygamous libellulid dragonfly Orthetrum coerulescens, we detected and quantified mixed paternity in sequentially produced offspring clutches and demonstrated that fertilization success is correlated with the duration of copulation. Our results suggest that RAPD fingerprinting is suitable to address issues of paternity in systems which are genetically uncharacterized and produce large offspring clutches.