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Open Access Publications from the University of California

Scholarly Works (11 results)

  • Article
  • Peer Reviewed
Structure and Dynamics, Volume 1, Issue 2 (2005)

While we typically count the number of people directly affected by violence, war and state action with casualty reports, we often ignore how these people are embedded in larger networks. In this paper, I estimate the number of people who know somebody who has been killed, injured or detained in the US war on terrorism in Iraq and Afghanistan, and thus likely at higher risk to joining a resistance movement. Since such numbers are constantly changing, an on-line web-calculator for the estimates is included so that readers can make their own estimates as well. Better understanding how friends and families are affected by such actions will help us understand the wider implications of military action.

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Cover page: Fighting a Hydra: A Note on the Network Embeddedness of the War on Terror
  • Article
  • Peer Reviewed
UC Irvine Previously Published Works (2003)
Although questions about social cohesion lie at the core of our discipline, definitions are often vague and difficult to operationalize. Here, research on social cohesion and social embeddedness is linked by developing a concept of structural cohesion based on network node connectivity. Structural cohesion is defined as the minimum number of actors who, if removed from a group, would disconnect the group. A structural dimension of embeddedness can then be defined through the hierarchical nesting of these cohesive structures. The empirical applicability of nestedness is demonstrated in two dramatically different substantive settings, and additional theoretical implications with reference to a wide array of substantive fields are discussed.
    Cover page: Structural Cohesion and Embeddedness: A Hierarchical Concept of Social GroupsCreative Commons 'BY' version 4.0 license
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2019)

    We investigate structures of size at most continuum using various techniques originating from computable structure theory and continuous logic. Our approach, which we are naming ``computable continuous structure theory", allows the fine-grained tools of computable structure theory to be generalized to apply to a wide class of separable completely-metrizable structures, such as Hilbert spaces, the p-adic integers, and many others. We can generalize many ideas, such as effective Scott families and effective type-omitting, to this wider class of structures. Since our logic respects the underlying topology of the space under consideration, it is in some sense more natural for structures with a metrizable topology which is not discrete.

      Cover page: Computable Continuous Structure Theory
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2016)
      Structurally cohesive subgroups are a powerful and mathematically rigorous way to characterize network robustness. Their strength lies in the ability to detect strong connections among vertices that not only have no neighbors in common, but that may be distantly separated in the graph. Unfortunately, identifying cohesive subgroups is a computationally intensive problem, which has limited empirical assessments of cohesion to relatively small graphs of at most a few thousand vertices. We describe here an approach that exploits the properties of cliques, k-cores and vertex separators to iteratively reduce the complexity of the graph to the point where standard algorithms can be used to complete the analysis. As a proof of principle, we apply our method to the cohesion analysis of a 29,462-vertex biconnected component extracted from a 128,151-vertex co-authorship data set.
        Cover page: Fast determination of structurally cohesive subgroups in large networks
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2004)

        Social action is situated in fields that are simultaneously composed of interpersonal ties and relations among organizations, which are both usefully characterized as social networks. We introduce a novel approach to distinguishing different network macro-structures in terms of cohesive subsets and their overlaps. We develop a vocabulary that relates different forms of network cohesion to field properties as opposed to organizational constraints on ties and structures. We illustrate differences in probabilistic attachment processes in network evolution that link on the one hand to organizational constraints versus field properties and to cohesive network topologies on the other. This allows us to identify a set of important new micro-macro linkages between local behavior in networks and global network properties. The analytic strategy thus puts in place a methodology for Predictive Social Cohesion theory to be developed and tested in the context of informal and formal organizations and organizational fields. We also show how organizations and fields combine at different scales of cohesive depth and cohesive breadth. Operational measures and results are illustrated for three organizational examples, and analysis of these cases suggests that different structures of cohesive subsets and overlaps may be predictive in organizational contexts and similarly for the larger fields in which they are embedded. Useful predictions may also be based on feedback from level of cohesion in the larger field back to organizations, conditioned on the level of multiconnectivity to the field.

          Cover page: Networks, Fields and Organizations: Micro-Dynamics, Scale and Cohesive Embeddings.
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2021)

          Objectives

          Women may differ by whether they rely on health providers and/or social ties for seeking information and advice about family planning. It is unknown whether these differences matter for contraceptive outcomes. This study assessed the association between women's family planning (FP) network (social and/or provider ties) and contraceptive use.

          Study design

          This cross-sectional, egocentric network study was conducted among reproductive-age women (n = 193) in rural Madagascar. Data included socio-demographics and contraceptive use. Respondents listed who they relied on for contraceptive information, advice or guidance and provided ties' gender, age, relationship, and perceived support of contraceptive use. The primary outcome was current contraceptive use. Predictors included having a FP network (0/1) and FP network composition (no network, social ties only, provider ties only, both provider and social ties), respectively. Analyses were conducted using a generalized linear model specifying a Poisson distribution, with covariate adjustment and cluster robust standard errors.

          Results

          Having a network of individuals to turn to for contraceptive information compared to having no FP network was positively associated with contraceptive use (adjusted relative risk [aRR] 4.4, 95% confidence interval [CI] 2.00-9.87). Having a social network, a provider network, or a combination of social and provider network were all positively associated with contraceptive use (aRR 4.30 [CI 1.92-9.66], aRR 4.46 [CI 2.04-9.75], aRR 4.72 [CI 1.93-11.50], respectively), compared to having no FP network.

          Conclusions

          Contraceptive use was higher among women who relied on social ties, provider ties or both for contraceptive information and advice, compared to women with no FP network. These findings suggest that FP interventions should use a multicomponent approach taking into account both social and provider networks.

          Implications

          It is unknown whether differences in whether women rely on social ties (friends, partner, family members) vs. providers for contraceptive information and advice affect contraceptive outcomes. Women are just as likely to use contraception whether they rely on social ties, provider ties, or both for contraceptive information and advice.
            Cover page: Social and provider networks and women's contraceptive use: Evidence from Madagascar
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2021)

            Background

            Ensuring women have information, support and access to family planning (FP) services will allow women to exercise their reproductive autonomy and reduce maternal mortality, which remains high in countries such as Madagascar. Research shows that women's social networks - their ties with partners, family members, friends, and providers - affect their contraceptive use. Few studies have considered the role of men's social networks on women's contraceptive use. Insofar as women's contraceptive use may be influenced by their male partners, women's contraceptive use may also be affected by their partner's social networks. Men may differ by the types of ties they rely on for information and advice about FP. It is unknown whether differences in the composition of men's FP networks matter for couples' contraceptive use. This study assessed the association between men's FP networks and couples' contraceptive use.

            Methods

            This egocentric network study was conducted among married/partnered men (n = 178) in rural Madagascar. Study participants listed who they relied on for FP information and advice, including health providers and social ties. They provided ties' gender, age, relationship, and perceived support of contraceptive use. The primary outcome was couples' contraceptive use, and explanatory variables included FP networks and their composition (no FP network, social-only network, provider-only network, and mixed network of social and provider ties). Analyses used generalized linear models specifying a Poisson distribution, with covariate adjustment and cluster robust standard errors.

            Results

            Men who had FP networks were 1.9 times more likely to use modern contraception as a couple compared to men with no FP network (95% confidence interval [CI] 1.64-2.52; p ≤ 0.001). Compared to men with no FP network, men were more likely to use modern contraception if they had a social-only network, relative risk (RR) = 2.10 (95% CI, 1.65-2.68; p ≤ 0.001); a provider-only network, RR = 1.80 (95% CI, 1.54-2.11; p ≤ 0.001); or a mixed network, RR = 2.35 (95% CI, 1.97-2.80; p ≤ 0.001).

            Conclusions

            Whether men have a FP network, be it provider or social ties, distinguishes if couples are using contraception. Interventions should focus on reaching men not only through providers but also through their social ties to foster communication and support for contraceptive use.
              Cover page: The association between men’s family planning networks and contraceptive use among their female partners: an egocentric network study in Madagascar
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2020)

              Background

              HIV-infected youth in sub-Saharan Africa are less likely to initiate antiretroviral therapy (ART) than older adults.

              Setting and methods

              Adult (≥15 years) residents enumerated during a census in 32 communities in rural Kenya and Uganda named social contacts in 5 domains: health, money, emotional support, food, and free time. Named contacts were matched to other enumerated residents to build social networks among 150,395 adults; 90% were tested for HIV at baseline. Among youth (15-24 years) who were ART naive at baseline (2013-2014), we evaluated whether having ≥1 network contact who was HIV infected predicted ART initiation within 3 years and modification of this association by age and strength of contact, using logistic regression with robust standard errors.

              Results

              Among 1120 HIV-infected youth who were ART naive at baseline, 805 remained alive and community residents after 3 years. Of these, 270 (33.5%) named at least one baseline HIV-infected contact; 70% (569/805) subsequently initiated ART. Youth with ≥1 HIV-infected same-age baseline contact were more likely to initiate ART [adjusted odds ratio (aOR), 2.95; 95% confidence interval (CI): 1.49 to 5.86] than those with no HIV-infected contact, particularly if the contact was a strong tie (named in >1 domain; aOR, 5.33; 95% CI: 3.34 to 8.52). When nonhousehold contacts were excluded, having an HIV-infected same age contact who was a strong tie remained associated with ART initiation (aOR, 2.81; 95% CI: 1.76 to 4.49).

              Conclusions

              Interventions that increase and strengthen existing social connections to other HIV-infected peers at the time of HIV diagnosis may increase ART initiation among HIV-infected youth.
                Cover page: The Influence of Social Networks on Antiretroviral Therapy Initiation Among HIV-Infected Antiretroviral Therapy-Naive Youth in Rural Kenya and Uganda.
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2022)
                Early and appropriate use of antenatal care services is critical for reducing maternal and neonatal mortality and morbidity. Yet most women in sub-Saharan Africa, including Uganda, do not seek antenatal care until later during pregnancy. This qualitative study explored pregnant women's reliance on social ties for information about initiation of antenatal care. We conducted semi-structured, in-depth interviews with 30 pregnant women seeking their first antenatal care visit at Kawempe Referral Hospital in Kampala, Uganda. Recruitment was done purposively to obtain variation by parity and whether women currently had a male partner. Study recruitment occurred from August 25th 2020 - October 26th, 2020. We used thematic analysis following a two-stage coding process, with both deductive and inductive codes. Deductive codes followed the key domains of social network and social support theory. We found that the most important source of information about antenatal care initiation was these women's mothers. Other sources included their mothers-in-law, female elders including grandmothers, and male partners. Sisters and female friends were less influential information sources about antenatal initiation. One of the primary reasons for relying on their own mothers, mothers-in-law, and elder women was due to these women's lived experience with pregnancy and childbirth. Trust in the relationship was also an important factor. Some pregnant women were less likely to rely on their sisters or female friends, either due to lack of trust or these women's lack of experience with pregnancy and childbirth. The advice that pregnant women received from their mothers and others on the ideal timing for antenatal care initiation varied significantly, including examples of misinformation about when to initiate antenatal care. Pregnant women seemed less likely to delay care when more than one social tie encouraged early antenatal care. Educating women's social networks, especially their mothers, mothers-in-law, and community elders, about the importance of early antenatal care initiation is a promising avenue for encouraging pregnant women to seek care earlier in pregnancy.
                  Cover page: The role of informational support from women’s social networks on antenatal care initiation: qualitative evidence from pregnant women in Uganda
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2024)
                  Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase, and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, demonstrate complex formation between TclI, TclJ, and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core.

                  Importance

                  Thiopeptides are a family of antimicrobial peptides characterized for having sulfur-containing heterocycles and for being highly post-translationally modified. Numerous thiopeptides have been identified; almost all of which inhibit protein synthesis in gram-positive bacteria. These intrinsic antimicrobial properties make thiopeptides promising candidates for the development of new antibiotics. The thiopeptide micrococcin is synthesized by the ribosome and undergoes several post-translational modifications to acquire its bioactivity. In this study, we identify key interactions within the enzymatic complex that carries out cysteine to thiazole conversion in the biosynthesis of micrococcin.
                    Cover page: Micrococcin cysteine-to-thiazole conversion through transient interactions between the scaffolding protein TclI and the modification enzymes TclJ and TclN.Creative Commons 'BY' version 4.0 license
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