Compendium of human transcription factor effector domains.

Transcription factors (TFs) regulate gene expression by binding to DNA sequences and modulating transcriptional activity through their effector domains. Despite the central role of effector domains in TF function, there is a current lack of a comprehensive resource and characterization of effector domains. Here, we provide a catalog of 924 effector domains across 594 human TFs. Using this catalog, we characterized the amino acid composition of effector domains, their conservation across species and across the human population, and their roles in human diseases. Furthermore, we provide a classification system for effector domains that constitutes a valuable resource and a blueprint for future experimental studies of TF effector domain function.

Differences between the geometric phase and propagation phase: clarifying the boundedness problem.

We show white light interferometer experiments that clearly demonstrate the basic differences between geometric and propagation phases. These experimental results also suggest a way to answer the "boundedness problem" in geometric phase-whether geometric phase is unbounded (i.e., can take on any values without limit) or bounded (i.e., limited to values between -π and +π). We show why the answer to this question is not as easy as it seems, from both a theoretical and an experimental perspective, and explain how the answer depends on one's choice of phase convention. We also hope that the videos provided will be pedagogically useful for explaining geometric phase.

Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas.

BACKGROUND: Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS: The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS: The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.

Efficient line shape estimation by ghost spectroscopy.

Recovering the original spectral line shapes from data obtained by instruments with extended transmission profiles is a basic tenet in spectroscopy. By using the moments of the measured lines as basic variables, we turn the problem into a linear inversion. However, when only a finite number of these moments are relevant, the rest of them act as nuisance parameters. These can be taken into account with a semiparametric model, which allows us to establish the ultimate bounds on the precision attainable in the estimation of the moments of interest. We experimentally confirm these limits with a simple ghost spectroscopy demonstration.

Deciphering Pancharatnam's discovery of geometric phase: retrospective.

While Pancharatnam discovered the geometric phase in 1956, his work was not widely recognized until its endorsement by Berry in 1987, after which it received wide appreciation. However, because Pancharatnam's paper is unusually difficult to follow, his work has often been misinterpreted as referring to an evolution of states of polarization, just as Berry's work focused on a cycle of states, even though this consideration does not appear in Pancharatnam's work. We walk the reader through Pancharatnam's original derivation and show how Pancharatnam's approach connects to recent work in geometric phase. It is our hope to make this widely cited classic paper more accessible and better understood.

Wave description of geometric phase.

Since Pancharatnam's 1956 discovery of optical geometric phase and Berry's 1984 discovery of geometric phase in quantum systems, researchers analyzing geometric phase have focused almost exclusively on algebraic approaches using the Jones calculus, or on spherical trigonometry approaches using the Poincaré sphere. The abstracted mathematics of the former and the abstracted geometry of the latter obscure the physical mechanism that generates geometric phase. We show that optical geometric phase derives entirely from the superposition of waves and the resulting shift in the location of the wave maximum. This wave-based model provides a way to visualize how geometric phase arises from relationships between waves, and from the transformations induced by optical elements. We also derive the relationship between the geometric phase of a wave by itself and the phase exhibited by an interferogram, and provide the conditions under which the two match one another.

Impact on physical function of the +AGIL Barcelona program in community-dwelling older adults with cognitive impairment: an interventional cohort study.

BACKGROUND: Older adults with cognitive impairment (CI) have higher multimorbidity and frailty prevalence, lower functional status and an increased likelihood to develop dementia, non-cognitive deficits, and adverse health-related events. +AGIL, a real-world program for frail older adults in a primary care area of Barcelona, is a pragmatic, multi-component and integrated intervention implemented since 2016. It includes physical activity, nutrition, sleep hygiene, revision and adequacy of pharmacological treatment, detection of undesired loneliness and screening for CI; to improve physical function in community-dwelling older adults. We aimed to assess the + AGIL longitudinal impact on physical function among community-dwelling frail older persons with CI. METHODS: An interventional cohort study included data from all the + AGIL consecutive participants from July 2016 until March 2020. Based on the comprehensive geriatric assessment, participants were offered a tailored multi-component community intervention, including a 10-week physical activity program led by an expert physical therapist. Physical performance was measured at baseline, three and six months follow-up. The pre-post impact on physical function was assessed by paired sample t-test for repeated samples. Linear mixed models were applied to analyze the + AGIL longitudinal impact. P-values < 0.05 were considered statistically significant. RESULTS: 194 participants were included (82 with CI, based on previous diagnosis or the Mini-COG screening tool), 68% women, mean age 81.6 (SD = 5.8) yo. Participants were mostly independent in Activities of Daily Living (mean Barthel = 92.4, SD = 11.1). The physical activity program showed high adherence (87.6% attended ≥ 75% sessions). At three months, there was a clinically and statistically significant improvement in the Short Physical Performance Battery (SPPB) and its subcomponents in the whole sample and after stratification for CI [CI group improvements: SPPB = 1.1 (SD = 1.8) points, gait speed (GS) = 0.05 (SD = 0.13) m/s, Chair stand test (CST)=-2.6 (SD = 11.4) s. Non-CI group improvements: SPPB = 1.6 (SD = 1.8) points, GS = 0.08 (SD = 0.13) m/s, CST=-6.4 (SD = 12.1) seg]. SPPB and gait speed remained stable at six months in the study sample and subgroups. CI had no significant impact on SPPB or GS improvements. CONCLUSION: Our results suggest that older adults with CI can benefit from a multidisciplinary integrated and comprehensive geriatric intervention to improve physical function, a component of frailty.

From polarization multipoles to higher-order coherences.

We demonstrate that the multipoles associated with the density matrix are truly observable quantities that can be unambiguously determined from intensity moments. Given their correct transformation properties, these multipoles are the natural variables to deal with a number of problems in the quantum domain. In the case of polarization, the moments are measured after the light has passed through two quarter-wave plates, one half-wave plate, and a polarizing beam splitter for specific values of the angles of the wave plates. For more general two-mode problems, equivalent measurements can be performed.

Anticaustics in a Fabry-Perot interferometer.

We address the response of a Fabry-Perot interferometer to a monochromatic point source. We calculate the anticaustics (that is, the virtual wavefronts of null path difference) resulting from the successive internal reflections occurring in the system. They turn out to be a family of ellipsoids (or hyperboloids) of revolution, which allows us to reinterpret the operation of the Fabry-Perot interferometer from a geometrical point of view that facilitates comparison with other apparently disparate arrangements, such as Young's double slit.

Seasonality of reproduction in wild cotton-top tamarins (Saguinus oedipus) in Colombia.

Seasonal availability of resources can influence the timing and success of reproduction in primates. This study examines the annual pattern of conceptions, mid-term (13 weeks) and full-term (26 weeks) pregnancy losses, births, and infant survivorship of the Critically Endangered cotton-top tamarin (Saguinus oedipus) at Proyecto Tití's long-term field site in Santa Catalina, Colombia. Using 18 years of behavior, physical exam, and fecal steroid data (N = 51 females, 168 conceptions, 121 liters), fecal estrone conjugate (E1 C) and pregnanediol-3-glucuronide (PdG) or progesterone (P4) profiles were examined to investigate the relationships between female reproductive patterns and reproductive success with feeding and climatic data. Cotton-top tamarins demonstrated seasonal patterns of reproduction and pregnancy losses. We found positive correlations between peak conception and nectarivory, births and rainfall, and mid-lactation and frugivory. High body mass mothers reproducing during the peak season were more likely to have infants survive. Overall, these results suggest that tamarins use a "relaxed income-breeder" strategy. Cotton-top tamarins appear to maximize reproductive output at the time of ovulation, and can reduce their investment in the current reproductive effort at many stages. Changes in food availability due to habitat loss and climate change will require the Critically Endangered cotton-top tamarins to alter their reproductive strategies to survive.

Sulfated Polysaccharide Extracted from the Green Algae Codium bernabei: Physicochemical Characterization and Antioxidant, Anticoagulant and Antitumor Activity.

Codium bernabei is a green alga that grows on Chilean coasts. The composition of its structural polysaccharides is still unknown. Hence, the aim of this work is to isolate and characterize the hot water extracted polysaccharide fractions. For this purpose, the water extracts were further precipitated in alcohol (TPs) and acid media (APs), respectively. Both fractions were characterized using different physicochemical techniques such as GC-MS, GPC, FTIR, TGA, and SEM. It is confirmed that the extracted fractions are mainly made of sulfated galactan unit, with a degree of sulfation of 19.3% (TPs) and 17.4% (ATs) and a protein content of 3.5% in APs and 15.6% in TPs. Other neutral sugars such as xylose, glucose, galactose, fucose, mannose, and arabinose were found in a molar ratio (0.05:0.6:1.0:0.02:0.14:0.11) for TPs and (0.05:0.31:1.0:0.03:0.1:0.13) for ATs. The molecular weight of the polysaccharide samples was lower than 20 kDa. Both polysaccharides were thermally stable (Tonset > 190 °C) and showed antioxidant activity according to the ABTS•+ and DPPH tests, where TPs fractions had higher scavenging activity (35%) compared to the APs fractions. The PT and APTTS assays were used to measure the anticoagulant activity of the polysaccharide fractions. In general, the PT activity of the TPs and APs was not different from normal plasma values. The exception was the TPs treatment at 1000 µg mL−1 concentration. The APTTS test revealed that clotting time for both polysaccharides was prolonged regarding normal values at 1000 µg mL−1. Finally, the antitumor test in colorectal carcinoma (HTC-116) cell line, breast cancer (MCF-7) and human leukemia (HL-60) cell lines showed the cytotoxic effect of TPs and APs. Those results suggest the potential biotechnological application of sulfate galactan polysaccharides isolated from a Chilean marine resource.

Efficiency of an up-flow Anaerobic Sludge Blanket reactor coupled with an electrochemical system to remove chloramphenicol in swine wastewater.

The application and design of treatment systems in wastewater are necessary due to antibiotics' potential toxicity and resistant genes on residual effluent. This work evaluated a coupled bio-electrochemical system to reduce chloramphenicol (CAP) and chemical oxygen demand (COD) on swine wastewater (SWW). SWW characterization found CAP of <10 µg/L and 17,434 mg/L of COD. The coupled system consisted of preliminary use of an Up-flow Anaerobic Sludge Blanket Reactor (UASB) followed by electrooxidation (EO). The UASB reactor (primary stage) was operated for three months at an organic load of 8.76 kg of COD/m3d and 50 mg CAP/L as initial concentration. In EO, we carried out a 22 (time operation and intensity) factorial design with a central composite design; we tried two Ti cathodes and one anode of Ti/PbO2. Optimal conditions obtained in the EO process were 240 min of operation time and 1.51 A of current intensity. It was possible to eliminate 44% of COD and 64.2% of CAP in the preliminary stage. On bio-electrochemicals, total COD and CAP removal were 82.35 and >99.99%, respectively. This coupled system can be applied to eliminate antibiotics and other organic pollutants in agricultural, industrial, municipal, and other wastewaters.

Intrinsic Sensitivity Limits for Multiparameter Quantum Metrology.

The quantum Cramér-Rao bound is a cornerstone of modern quantum metrology, as it provides the ultimate precision in parameter estimation. In the multiparameter scenario, this bound becomes a matrix inequality, which can be cast to a scalar form with a properly chosen weight matrix. Multiparameter estimation thus elicits trade-offs in the precision with which each parameter can be estimated. We show that, if the information is encoded in a unitary transformation, we can naturally choose the weight matrix as the metric tensor linked to the geometry of the underlying algebra su(n), with applications in numerous fields. This ensures an intrinsic bound that is independent of the choice of parametrization.

Factors influencing the survival of wild cotton-top tamarin (Saguinus oedipus) infants.

Studies of cooperative breeding species have suggested that helpers are needed for infant survival and that helpers gain skills to successfully raise their own offspring. Studies of callitrichids in managed care and early field studies suggested that group size correlated with infant survival and that helpers needed to learn parental skills to be successful breeders. We present infant survival data from a 20-year field study of cotton-top tamarins (Saguinus oedipus) in Colombia involving 126 litters born to 41 females. There was no difference in the survival of male and female offspring to 6 months of age. However, litter size impacted survival, with triplet litters having lower survival and male triplets having lower survival than females. Loss of infants was highest in the first week of life and, of the animals remaining in the group at 6 months of age, 90% of them survived to 1 year. The mean length of time in the natal group was 2.3 years but some young migrated to other groups after 4 months of age. Group size and number of male helpers (>1 year) was not related to infant survival. However, groups with only one male had fewer surviving infants. Primiparous females had lower infant survival, but previous infant care experience by mothers as helpers had no effect on survival. A major cause of infant loss was group disruption due to deaths/evictions/loss of the reproductively active animals, or immigration of pregnant females. Thus, factors that cause a change in the stability of the reproductively active animals can disrupt group cohesion. Capture of individuals for the illegal pet trade, as well as habitat fragmentation, may increase competition between groups for access to territories and breeding opportunities. This may have long-term impacts to infant survival in this critically endangered species.

Universal Compressive Characterization of Quantum Dynamics.

Recent quantum technologies utilize complex multidimensional processes that govern the dynamics of quantum systems. We develop an adaptive diagonal-element-probing compression technique that feasibly characterizes any unknown quantum processes using much fewer measurements compared to conventional methods. This technique utilizes compressive projective measurements that are generalizable to an arbitrary number of subsystems. Both numerical analysis and experimental results with unitary gates demonstrate low measurement costs, of order O(d^{2}) for d-dimensional systems, and robustness against statistical noise. Our work potentially paves the way for a reliable and highly compressive characterization of general quantum devices.

Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.

Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.

Compressed sensing of twisted photons.

The ability to completely characterize the state of a system is an essential element for the emerging quantum technologies. Here, we present a compressed-sensing-inspired method to ascertain any rank-deficient qudit state, which we experimentally encode in photonic orbital angular momentum. We efficiently reconstruct these qudit states from a few scans with an intensified CCD camera. Since it only requires a small number of intensity measurements, our technique provides an easy and accurate way to identify quantum sources, channels, and systems.

A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria.

Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.

Zika Virus in the Americas: An Environmental Health Perspective.

Phylogenetic studies suggest that ZIKV may have been introduced to Brazil, and therefore to the Americas, in 2014 during the World Spring Canoe Championship held in the city of Rio de Janeiro. Since then the virus has spread across Latin America, Caribbean, and North America. It seems clear that Aedes aegypti and, to a lesser extent, Aedes albopictus are the main vectors of the pathogen. ZIKV infection symptoms are similar to other flaviviruses such as a dengue infection and therefore can be easily confounded. Currently, the ZIKV maintains two life cycles. The first, and the original one is the sylvatic/enzootic cycle that occurs in Africa. The second life cycle is the suburban-urban transmission cycle that emerged through natural evolution. ZIKV has gained the ability to maintain this human-endemic cycle in urban and suburban areas. ZIKV has never been isolated from non primates, so it is not clear whether other species can act as reservoir hosts. Several reports have been made of non-vector ZIKV transmission including breast-milk feeding, blood transfusion, sexual intercourse, saliva, urine, and physical contact (sweat, tears). A major global concern with ZIKV infection is the reported increase in cases of microcephaly and Guillain-Barre Syndrome (GBS) in the Americas after the recent ZIKV outbreak. Currently, there is no available vaccine for ZIKV. Therefore, prevention of ZIKV infection must be emphasized by local public health authorities promoting collective responsibility and engagement for integrated vector management through environmental management, biological control, and as a last resource chemical control.

The Role of Research in Policy and Practice: The Zika Phenomena in Puerto Rico.

On April 19, 2017, the 37th Medical Sciences Campus Annual Research and Education Forum opened with the discussion panel The role of research in policy and practice: The Zika phenomena in Puerto Rico, with Dr. Cruz M. Nazario Delgado, Dr. Carmen D. Zorrilla and Dr. Luis A. Bonilla Soto. In this article, we critically examine the public policy process of the Zika epidemic in Puerto Rico, as presented by authors Nazario and Bonilla. We argue that policymaking and the public health responses to confront the Zika epidemic in Puerto Rico took place in a political environment where different US and local actors operated to advance their goals and vision, undermining the role of knowledge, evidence and past experiences. We propose a bottom to top preventive and community empowerment approach to control the vector. This model must be built on successful policy implementation experiences with epidemics in the Island and strengthened by evidence, international guidelines and ethical principles.